Re: [R] rpart cutpoint interpretation

[Kishor Tappita]

Thank you so much for the clarification Terry.

On Thu, Oct 8, 2015 at 6:03 PM, Therneau, Terry M., Ph.D.  wrote:

> The cutpoint is on the predictor, so the interpretation is the same as it
> is for any other rpart model.  The subjects with predictor < cutpoint form
> one group and those > cutpoint the other.  The cutpoint is chosen to give
> the greatest difference in "average y" between the groups.  For poisson
> "averge y" is an event rate.
>
>
> On 10/08/2015 05:00 AM, r-help-requ...@r-project.org wrote:
>
>> I am trying to derive cutpoint/threshold with a poisson distributed
>> dependent variable. I know how to interpret cutpoint with binary dependent
>> variable based on direction. Can some on help me to intrepret cutpoint for
>> poisson case with one independent variable with the derived threshold.
>>
>

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[R] rpart cutpoint interpretation

[Kishor Tappita]

Hi All,

I am trying to derive cutpoint/threshold with a poisson distributed
dependent variable. I know how to interpret cutpoint with binary dependent
variable based on direction. Can some on help me to intrepret cutpoint for
poisson case with one independent variable with the derived threshold.

Thanks in advance.

Regards,
Kishor

[[alternative HTML version deleted]]

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[R] BioNet::runFastHeinz error

[Kishor Tappita]

Dear R-Users,

I am trying to perform network analysis using BioNet. I am having
issues with the runFastHeinz function. I extracted the sub network and
computed the scores and fed to the function. I even tried to run the
function from the example data in the help function. I get the same
error. Please help me solve this issue. I tried accessing the
igraph.from.graphNEL function from igraph as
igraph::igraph.from.graphNEL. But still it didnt fix the error.

library(DLBCL)
data(dataLym)
data(interactome)
interactome - subNetwork(dataLym$label, interactome)
p.values - dataLym$t.pval
names(p.values) - dataLym$label
bum - fitBumModel(p.values, plot=TRUE)
scores - scoreNodes(network=interactome, fb=bum, fdr=0.0001)
module - runFastHeinz(network=interactome, scores=scores)

Error in graph[[9]][[3]] : subscript out of bounds

 sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_SG   LC_NUMERIC=C LC_TIME=en_SG
 [4] LC_COLLATE=en_SG LC_MONETARY=en_SGLC_MESSAGES=en_SG
 [7] LC_PAPER=C   LC_NAME=CLC_ADDRESS=C
[10] LC_TELEPHONE=C   LC_MEASUREMENT=en_SG LC_IDENTIFICATION=C

attached base packages:
[1] grid  stats graphics  grDevices utils datasets  methods
[8] base

other attached packages:
 [1] hash_2.2.6  DLBCL_1.3.5 BioNet_1.18.0
 [4] RBGL_1.34.0 Biobase_2.18.0  BiocGenerics_0.4.0
 [7] igraph0_0.5.5-3 maanova_1.28.0  samr_2.0
[10] matrixStats_0.8.12  impute_1.32.0   limma_3.14.4
[13] Rgraphviz_2.2.1 graph_1.36.2GeneNet_1.2.8
[16] igraph_0.6.6fdrtool_1.2.11  longitudinal_1.1.8
[19] corpcor_1.6.6   BiocInstaller_1.8.3

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.20.7 DBI_0.2-7IRanges_1.16.6
[4] parallel_2.15.1  R.methodsS3_1.5.2RSQLite_0.11.4
[7] stats4_2.15.1tools_2.15.1


Thanks,
Regards,
Kishor

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[R] ordinal data with binary response

[Kishor Tappita]

Dear R-users,

I am trying to analyze data with ordinal independent variables and
binary response . Could some one suggest me an appropriate statistic
for this kind of analysis.

Thanks,
Regards,
Kishir

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Re: [R] ordinal data with binary response

[Kishor Tappita]

Dear John,

Thanks for the information. It is quite helpful.

Regards,
Kishor

On Thu, Oct 24, 2013 at 9:24 PM, John Sorkin
jsor...@grecc.umaryland.edu wrote:
 Kishor,
 It sounds like you will need to use logistic regression. Although the
 following URL might help you better understand logistic regression,
 http://ww2.coastal.edu/kingw/statistics/R-tutorials/logistic.html  it would
 probably be most helpful if you would see help from a local statistician.
 John


 John David Sorkin M.D., Ph.D.
 Professor of Medicine
 Chief, Biostatistics and Informatics
 University of Maryland School of Medicine Division of Gerontology and
 Geriatric Medicine
 Baltimore VA Medical Center
 10 North Greene Street
 GRECC (BT/18/GR)
 Baltimore, MD 21201-1524
 (Phone) 410-605-7119
 (Fax) 410-605-7913 (Please call phone number above prior to faxing)
 Kishor Tappita kishor.tapp...@gmail.com 10/24/2013 5:15 AM 

 Dear R-users,

 I am trying to analyze data with ordinal independent variables and
 binary response . Could some one suggest me an appropriate statistic
 for this kind of analysis.

 Thanks,
 Regards,
 Kishir

 __
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 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


 Confidentiality Statement:

 This email message, including any attachments, is for ...{{dropped:6}}

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[R] problem installing RDCOMEvents

[Kishor Tappita]

Dear R-Users,

I am getting the below error when I am trying to install RDCOMEvents
from Omegahat. All the dependencies were installed .Please help me
resolve this issue.

 library(RDCOMEvents)
Loading required package: RDCOMServer
Loading required package: SWinRegistry

Attaching package: 'SWinRegistry'


The following object(s) are masked from package:base :

 append

Loading required package: Ruuid
Loading required package: RDCOMClient
Loading required package: SWinTypeLibs
Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source
= keep.source) :
  in 'RDCOMEvents' methods for export not found: findConnectionPoint,
createCOMEventServer
In addition: There were 18 warnings (use warnings() to see them)
Error: package/namespace load failed for 'RDCOMEvents'

 sessionInfo()
R version 2.9.1 (2009-06-26)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] SWinTypeLibs_0.5-1 RDCOMClient_0.92-0 RDCOMServer_0.6-2  Ruuid_1.22.0
[5] SWinRegistry_0.3-3


Thanks,
Regards,
Kishor

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Re: [R] problem installing RDCOMEvents

[Kishor Tappita]

Dear Prof Ripley,

Thanks for your reply. I tried with R -versions (R-3.0.1  R-2.15.2)
but was having problem with installing the dependencies such as
SWinRegistry,SWinTypeLibs. With R version 2.9.1, I was able to install
all the dependencies but am having problem with installing
RDCOMEvents.

As suggested by you I will contact the package maintainer.

Thanks,
Regards,
Kishor


On Fri, Aug 16, 2013 at 3:29 PM, Prof Brian Ripley
rip...@stats.ox.ac.uk wrote:
 Are you serious: 'R version 2.9.1 (2009-06-26)' ?

 Please see the posting guide (see the footer of this message), and

 1) Update your R.

 2) If this still does not work, ask the package maintainer.



 On 16/08/2013 09:29, Kishor Tappita wrote:

 Dear R-Users,

 I am getting the below error when I am trying to install RDCOMEvents
 from Omegahat. All the dependencies were installed .Please help me
 resolve this issue.

 library(RDCOMEvents)

 Loading required package: RDCOMServer
 Loading required package: SWinRegistry

 Attaching package: 'SWinRegistry'


  The following object(s) are masked from package:base :

   append

 Loading required package: Ruuid
 Loading required package: RDCOMClient
 Loading required package: SWinTypeLibs
 Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source
 = keep.source) :
in 'RDCOMEvents' methods for export not found: findConnectionPoint,
 createCOMEventServer
 In addition: There were 18 warnings (use warnings() to see them)
 Error: package/namespace load failed for 'RDCOMEvents'

 sessionInfo()

 R version 2.9.1 (2009-06-26)
 i386-pc-mingw32

 locale:
 LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
 States.1252;LC_MONETARY=English_United
 States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods   base

 other attached packages:
 [1] SWinTypeLibs_0.5-1 RDCOMClient_0.92-0 RDCOMServer_0.6-2  Ruuid_1.22.0
 [5] SWinRegistry_0.3-3


 Thanks,
 Regards,
 Kishor

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.



 --
 Brian D. Ripley,  rip...@stats.ox.ac.uk
 Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
 University of Oxford, Tel:  +44 1865 272861 (self)
 1 South Parks Road, +44 1865 272866 (PA)
 Oxford OX1 3TG, UKFax:  +44 1865 272595

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem installing RDCOMClient on Windows 7

[Kishor Tappita]

Dear Uwe,

Thank you for your repsonse. I installed the latest version of R
(R-3.0.1) . I get the below errors when I try to install RDCOMClient.

g++ -m32 -ID:/R-3.0.1/include -DNDEBUG -D_GNU_ -DNO_PYCOM_IPROVIDECLASSINFO -
.-Id:/RCompile/CRANpkg/extralibs64/local/include  -Wno-deprecated-O2
Wall  -mtune=core2 -c connect.cpp -o connect.o
In file included from d:\mingw\bin\../lib/gcc/mingw32/4.6.2/include/c++/cstdio:
4:0,
 from D:/R-3.0.1/include/Rinternals.h:25,
 from D:/R-3.0.1/include/Rdefines.h:29,
 from RUtils.h:1,
 from connect.cpp:20:
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:573:9:
error: 'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:574:9:
error:'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:575:9:
error:'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:586:9:
error:'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:587:9: error:
'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:589:9: error:
'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:591:9: error:
'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:632:9: error:
'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:633:9: error:
'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:638:9: error:
'wint_t' does not name a type
d:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/stdio.h:639:9: error:
'wint_t' does not name a type
make: *** [connect.o] Error 1
ERROR: compilation failed for package 'RDCOMClient'
* removing 'D:/R-3.0.1/library/RDCOMClient'



 sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C   LC_TIME=English_United
States.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base


Thanks,
Regards,
Kishor



On Mon, Aug 5, 2013 at 9:03 PM, Uwe Ligges
lig...@statistik.tu-dortmund.de wrote:
 Please try with a recent version of R. Yours is 6 major updates behind

 Best,
 Uwe Ligges



 On 05.08.2013 16:11, Kishor Tappita wrote:

 Dear R-Users,

 I am trying to install RDCOMClient package as it is a dependency for
 installing excel.link package. I get the below error while trying to
 install RDCOMClient on 64-bit Windows 7 operating system.


 g++ -ID:/R-2.10.0/include -D_GNU_ -DNO_PYCOM_IPROVIDECLASSINFO -I.
   -Wno-deprecated-O2 -Wall  -c RUtils.c -o RUtils.o

 RUtils.c: In function 'SEXPREC* R_createRCOMUnknownObject(void*, const
 char*)':
 RUtils.c:151:52: error: invalid conversion from 'int' to 'Rboolean'
 [-fpermissive]
 D:/R-2.10.0/include/Rinternals.h:692:6: error:   initializing argument
 3 of 'void R_RegisterCFinalizerEx(SEXP, R_CFinalizer_t, Rboolean)'
 [-fpermissive]
 RUtils.c: In function 'Rboolean ISSInstanceOf(SEXP, const char*)':
 RUtils.c:245:26: error: invalid conversion from 'int' to 'Rboolean'
 [-fpermissive]

 make: *** [RUtils.o] Error 1

 Please help me to resolve this issue. RDCOMClient_0.93-0.tar.gz is the
 source file that I am using. Below is my session information.

 sessionInfo()

 R version 2.10.0 (2009-10-26)
 i386-pc-mingw32

 locale:
 [1] LC_COLLATE=English_United States.1252
 [2] LC_CTYPE=English_United States.1252
 [3] LC_MONETARY=English_United States.1252
 [4] LC_NUMERIC=C
 [5] LC_TIME=English_United States.1252

 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods   base

 Thanks,
 Kishor

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] problem installing RDCOMClient on Windows 7

[Kishor Tappita]

Dear R-Users,

I am trying to install RDCOMClient package as it is a dependency for
installing excel.link package. I get the below error while trying to
install RDCOMClient on 64-bit Windows 7 operating system.


g++ -ID:/R-2.10.0/include -D_GNU_ -DNO_PYCOM_IPROVIDECLASSINFO -I.
 -Wno-deprecated-O2 -Wall  -c RUtils.c -o RUtils.o

RUtils.c: In function 'SEXPREC* R_createRCOMUnknownObject(void*, const char*)':
RUtils.c:151:52: error: invalid conversion from 'int' to 'Rboolean'
[-fpermissive]
D:/R-2.10.0/include/Rinternals.h:692:6: error:   initializing argument
3 of 'void R_RegisterCFinalizerEx(SEXP, R_CFinalizer_t, Rboolean)'
[-fpermissive]
RUtils.c: In function 'Rboolean ISSInstanceOf(SEXP, const char*)':
RUtils.c:245:26: error: invalid conversion from 'int' to 'Rboolean'
[-fpermissive]

make: *** [RUtils.o] Error 1

Please help me to resolve this issue. RDCOMClient_0.93-0.tar.gz is the
source file that I am using. Below is my session information.

 sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

Thanks,
Kishor

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] mvpart - legend help

[Kishor Tappita]

Dear R-Users,

I was able to use mvpart package for my multi-response data and was able to
generate the decision tree.

I realized that the colors (3) for the legend are being recycled.  In my
situation I have 12
dependent variables and would like to have 12 different colors for the
legend and barplots.
Otherwise please help me understand the reason for having 3 colors.

And also at each node, I see two values,  1. the number of cases and
another number. Please help me understand
what the other number means.

Thanks in advance.


 sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

Regard,
Kishor

[[alternative HTML version deleted]]

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R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem with installing R pacakges

[Kishor Tappita]

Dear Uwe,

I will enter the correct user::password values and try again. As per your
suggestion I will contact the local sysadmin
if required.

Thanks for your help.

Regards,
Kishor

On Wed, Jul 18, 2012 at 12:46 AM, Uwe Ligges 
lig...@statistik.tu-dortmund.de wrote:



 On 16.07.2012 14:45, Kishor Tappita wrote:

 Dear R- Users,

 I am unable to install R packages over the internet. Below is my session
 information. My guess is that this may be
 a proxy issue. I have set the http_proxy_user : my user id(network id) :
 password (machine password) .



 Maybe not correctly?

 Please see what the R for Windows FAQs say about using proxies. If that
 does not help, ask your local sysadmin. We cannot help.

 Uwe Ligges



 The error I get is as below

  install.packages(MASS)

 Warning: unable to access index for repository
 http://ftp.iitm.ac.in/cran/**bin/windows/contrib/2.15http://ftp.iitm.ac.in/cran/bin/windows/contrib/2.15
 Warning: unable to access index for repository
 http://www.stats.ox.ac.uk/pub/**RWin/bin/windows/contrib/2.15http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.15
 Warning message:
 package ‘MASS’ is not available (for R version 2.15.1)

 Below is my session info. I searched in the archives but was not able to
 find the issue. Please excuse me if this
 is a repost.

  sessionInfo()

 R version 2.15.1 (2012-06-22)
 Platform: x86_64-pc-mingw32/x64 (64-bit)
 locale:
 [1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252
 LC_MONETARY=English_India.1252 LC_NUMERIC=C
 LC_TIME=English_India.1252
 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods   base
 loaded via a namespace (and not attached):
 [1] tools_2.15.1

 Thanks in advance.

 Regards,
 Kishor

 [[alternative HTML version deleted]]



 __**
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/**
 posting-guide.html http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.




[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] problem with installing R pacakges

[Kishor Tappita]

Dear R- Users,

I am unable to install R packages over the internet. Below is my session
information. My guess is that this may be
a proxy issue. I have set the http_proxy_user : my user id(network id) :
password (machine password) .

The error I get is as below

 install.packages(MASS)
Warning: unable to access index for repository
http://ftp.iitm.ac.in/cran/bin/windows/contrib/2.15
Warning: unable to access index for repository
http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.15
Warning message:
package ‘MASS’ is not available (for R version 2.15.1)

Below is my session info. I searched in the archives but was not able to
find the issue. Please excuse me if this
is a repost.

 sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252
LC_MONETARY=English_India.1252 LC_NUMERIC=C
LC_TIME=English_India.1252
attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base
loaded via a namespace (and not attached):
[1] tools_2.15.1

Thanks in advance.

Regards,
Kishor

[[alternative HTML version deleted]]

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Survival Analysis

[Kishor Tappita]

Dear David,

Thank you for your reply. I realized that the summary  function can help me
in finding the the order of the curves.
The 0.95UCL (95% upper confidence level) column in particular seems to
follow the same pattern as the curves on the plot.

I am new to survival analysis, so  please correct me if I am wrong.

Thanks,
Kishor



On Mon, Jul 18, 2011 at 3:21 AM, David Winsemius dwinsem...@comcast.netwrote:


 On Jul 17, 2011, at 11:27 AM, Kishor Tappita wrote:

  Dear List,

 I used survival package of R and was able to generate KM plots. Now I need


  help in finding the top curve in a non-visualization way. I mean to say
 that
 I would like to know the order of curves through any existing methods
 rather
 than looking at the KM plots. I need this information as I am generating
 KM
 plots for thousands of genes.


 Why aren't you taking the KM estimate at a particular time?

 --
 David


 I would really appreciate if some one can direct me and help me.

 Thanks,
 Regards,
 Kishor

[[alternative HTML version deleted]]

 __**
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/**
 posting-guide.html http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


 David Winsemius, MD
 West Hartford, CT



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Re: [R] Survival Analysis

[Kishor Tappita]

Ok David, Thanks for clearing my misconception. Then could you please
suggest me how I could get the KM estimate for a time point. I remember
reading the formula
for calculating the KM. Do, I have to write a method to compute the KM
estimate or will the survival package provide it for me?


Thank you so much in advance.

Regards,
Kishor

On Mon, Jul 18, 2011 at 7:52 PM, David Winsemius dwinsem...@comcast.netwrote:


 On Jul 18, 2011, at 10:10 AM, Kishor Tappita wrote:

 Dear David,

 Thank you for your reply. I realized that the summary  function can help me
 in finding the the order of the curves.
 The 0.95UCL (95% upper confidence level) column in particular seems to
 follow the same pattern as the curves on the plot.


 That would not have been my prediction. The 95% UCL could be high simply
 because the sample size in that group was small.

 --
 David


 I am new to survival analysis, so  please correct me if I am wrong.

 Thanks,
 Kishor



 On Mon, Jul 18, 2011 at 3:21 AM, David Winsemius 
 dwinsem...@comcast.netwrote:


 On Jul 17, 2011, at 11:27 AM, Kishor Tappita wrote:

  Dear List,

 I used survival package of R and was able to generate KM plots. Now I
 need


  help in finding the top curve in a non-visualization way. I mean to say
 that
 I would like to know the order of curves through any existing methods
 rather
 than looking at the KM plots. I need this information as I am generating
 KM
 plots for thousands of genes.


 Why aren't you taking the KM estimate at a particular time?

 --
 David


 I would really appreciate if some one can direct me and help me.

 Thanks,
 Regards,
 Kishor

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 __**
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/**
 posting-guide.html http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


 David Winsemius, MD
 West Hartford, CT



 David Winsemius, MD
 West Hartford, CT



[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Survival Analysis

[Kishor Tappita]

Thanks a lot. I used survfit to generate KM plots but I will try to figure
out to find the corresponding returned value for KM estimate. Thank you for
your invaluable help.

On Mon, Jul 18, 2011 at 8:28 PM, David Winsemius dwinsem...@comcast.netwrote:


 On Jul 18, 2011, at 10:42 AM, Kishor Tappita wrote:

  Ok David, Thanks for clearing my misconception. Then could you please
 suggest me how I could get the KM estimate for a time point. I remember
 reading the formula
 for calculating the KM. Do, I have to write a method to compute the KM
 estimate or will the survival package provide it for me?


 ?survfit
 ?survfit.formula

 --
 david.




 Thank you so much in advance.

 Regards,
 Kishor

 On Mon, Jul 18, 2011 at 7:52 PM, David Winsemius dwinsem...@comcast.net
 wrote:

 On Jul 18, 2011, at 10:10 AM, Kishor Tappita wrote:

  Dear David,

 Thank you for your reply. I realized that the summary  function can help
 me in finding the the order of the curves.
 The 0.95UCL (95% upper confidence level) column in particular seems to
 follow the same pattern as the curves on the plot.


 That would not have been my prediction. The 95% UCL could be high simply
 because the sample size in that group was small.

 --
 David


 I am new to survival analysis, so  please correct me if I am wrong.

 Thanks,
 Kishor



 On Mon, Jul 18, 2011 at 3:21 AM, David Winsemius dwinsem...@comcast.net
 wrote:

 On Jul 17, 2011, at 11:27 AM, Kishor Tappita wrote:

 Dear List,

 I used survival package of R and was able to generate KM plots. Now I
 need

 help in finding the top curve in a non-visualization way. I mean to say
 that
 I would like to know the order of curves through any existing methods
 rather
 than looking at the KM plots. I need this information as I am generating
 KM
 plots for thousands of genes.

 Why aren't you taking the KM estimate at a particular time?

 --
 David


 I would really appreciate if some one can direct me and help me.

 Thanks,
 Regards,
 Kishor

   [[alternative HTML version deleted]]

 __**
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/**
 posting-guide.html http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

 David Winsemius, MD
 West Hartford, CT




 David Winsemius, MD
 West Hartford, CT



 David Winsemius, MD
 West Hartford, CT



[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Survival Analysis

[Kishor Tappita]

Dear List,

I used survival package of R and was able to generate KM plots. Now I need
help in finding the top curve in a non-visualization way. I mean to say that
I would like to know the order of curves through any existing methods rather
than looking at the KM plots. I need this information as I am generating KM
plots for thousands of genes.

I would really appreciate if some one can direct me and help me.

Thanks,
Regards,
Kishor

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Hmm Topology restriction

[Kishor Tappita]

Dear List,

We are using RHmm to cluster data through HMM. We would like to
restrict the transition matrix of HMM, to get hierarchical connections
between clusters. But, RHmm doesn't seem to support these
restrictions. Can any one suggest a library to do that.

Thanks,
Kishor

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Hmm Topology restriction

[Kishor Tappita]

Dear Ingmar,

Thanks a lot.

Regards,
Kishor

On Thu, Dec 2, 2010 at 6:39 PM, Ingmar Visser i.vis...@uva.nl wrote:
 depmixS4 enables linear constraints on parameters, best, Ingmar

 On Thu, Dec 2, 2010 at 12:01 PM, Kishor Tappita kishor.tapp...@gmail.com
 wrote:

 Dear List,

 We are using RHmm to cluster data through HMM. We would like to
 restrict the transition matrix of HMM, to get hierarchical connections
 between clusters. But, RHmm doesn't seem to support these
 restrictions. Can any one suggest a library to do that.

 Thanks,
 Kishor

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.