Re: [aroma.affymetrix] Re: FIRMAGene command
Hi Daniela.
> I definitely loaded the package and had a look at the help.start docs.
> Neverthelss, I wasn't able to work out my problems that I described in
> my previous post.
OK, so you've read the documentation. But, you haven't told us what
you didn't understand there. I can try and explain the docs to you
...
-
cls: variable giving the class (aligned with the columns or sample
names of the input object).
-
So, this says that you need to specify a vector which gives the
experimental group of your samples.
So, in my example, the sample names were:
> getNames(cs)
[1] "TisMap_Brain_01_v1_WTGene1""TisMap_Brain_02_v1_WTGene1"
[3] "TisMap_Brain_03_v1_WTGene1""TisMap_Breast_01_v1_WTGene1"
[5] "TisMap_Breast_02_v1_WTGene1" "TisMap_Breast_03_v1_WTGene1"
[snip]
which get converted to:
> cls<-gsub("TisMap_","",gsub("_0[1-3]_v1_WTGene1","",getNames(cs)))
> cls
[1] "Brain""Brain""Brain""Breast" "Breast" "Breast"
[snip]
And, with the 'cls' variable, I tell FIRMAGene() what group each
sample is from. You need to do the same for you 14 samples.
---
idsToUse: indices of the units to calculate FIRMAGene scores for.
---
In my example, all this does:
u <- which(getUnitNames(cdf) %in%
hgnetaffx$probeset_id[hgnetaffx$category == "main" &
hgnetaffx$total_probes > 7 & hgnetaffx$total_probes < 200])
... (assuming you've read in an appropriate file to hgnetaffx) ...
only uses the "main" category probeset (i.e. not the control
probesets), only probesets with >7 and <200 probes within them.
>> > I am not sure what is supposed to be stored in cls and u.
OK, so hopefully you are ok with whats spelled out above. Ask
questions, mentioning what you don't understand, if not.
>> > I’m a bit confused however, with what the whole “unique cdf set” is
>> > for and how plm is working. Can I save the plm data into a txt file?
You don't really need to understand the uniquifying. Its just a step
that needs to be done.
For general info on probe level models, you might look at the
references mentioned in fitPLM() or rma():
library(affyPLM)
?fitPLM
library(oligo)
?rma
In terms of saving the "plm data" (I assume you mean chip effects?),
you should breeze through the vignette for Gene 1.0 ST arrays. At the
end, it extracts the summarized data into a data frame:
http://aroma-project.org/node/38
... and you could output this to a text file using write.table().
Hope that helps.
Cheers,
Mark
On Fri, Mar 19, 2010 at 5:25 AM, dkny169 wrote:
> I definitely loaded the package and had a look at the help.start docs.
> Neverthelss, I wasn't able to work out my problems that I described in
> my previous post.
>
> On Mar 18, 1:58 pm, Henrik Bengtsson
> wrote:
>> Hi.
>>
>> On Thu, Mar 18, 2010 at 6:47 PM, dkny169 wrote:
>> > Unfortunately I cannot get to the docs, unless the same docs are
>> > stored under help.start()
>>
>> Please explain what the problem/error is. Note that you have to load
>> a package in order to use ?/help() on its methods, e.g.
>>
>> library("FIRMAGene");
>> ?FIRMAGene
>>
>> If you don't load it, you get something like:
>>
>> > ?FIRMAGene
>>
>> No documentation for 'FIRMAGene' in specified packages and libraries:
>> you could try '??FIRMAGene'
>>
>> The help is the same regardless if you access it via ?/help() or
>> help.start(). So, yes, you'll find the same information if you do
>> help.start() -> Packages -> FIRMAGene -> FIRMAGene
>>
>> /Henrik
>>
>>
>>
>> > I used following parameters:
>> >>plm <- RmaPlm(csNU)
>> >> plm
>> > [1] "RmaPlm: 0x22388540"
>> >>cls<-gsub("TisMap_","",gsub("_0(1-3)_v1_WTGene1","",getNames(cs)))
>> >>cls
>> > [1] "P.L_10" "P.L_11" "P.L_12" "P.L_14" "P.L_15" "P.L_16" "P.L_2"
>> > "P.L_3"
>> > [9] "P.L_4" "P.L_5" "P.L_6" "P.L_7" "P.L_8" "P.L_9"
>>
>> > I am not sure what is supposed to be stored in cls and u.
>> > I’m a bit confused however, with what the whole “unique cdf set” is
>> > for and how plm is working. Can I save the plm data into a txt file?
>> > Many thanks for your help.
>> > I really appreciate it.
>> > Daniela
>>
>> > On Mar 16, 4:57 pm, Mark Robinson wrote:
>> >> Hi Daniela.
>>
>> >> You haven't told us what inputs you've used for 'plm' and 'cls' ...
>> >> and what is stored in 'u'?
>>
>> >> Have you read the docs at:
>>
>> >> ?FIRMAGene
>>
>> >> Cheers,
>> >> Mark
>>
>> >> On 14-Mar-10, at 10:21 AM, dkny169 wrote:
>>
>> >> > Hello,
>> >> > I have a question regarding FIRMAGene. Executing the FIRMAGene
>> >> > command I get the following error:
>> >> >> fg<-FIRMAGene(plm, idsToUse=u, cls=cls)
>> >> > Gathering/calculating residuals.
>> >> > Reading units.
>> >> > Error in if (any(units < 1)) stop("Argument 'units' contains non-
>> >> > positive indices.") :
>> >> > missing value where TRUE/FALSE needed
>>
>> >> > The commands used right before are:
>>
>> >> >> monetaffx<-read.csv("MoEx-1_0-st-v1.na29.mm9.transcript.csv",
>> >> >> sep=",",skip=20, header=TR
[aroma.affymetrix] Re: FIRMAGene command
I definitely loaded the package and had a look at the help.start docs.
Neverthelss, I wasn't able to work out my problems that I described in
my previous post.
On Mar 18, 1:58 pm, Henrik Bengtsson
wrote:
> Hi.
>
> On Thu, Mar 18, 2010 at 6:47 PM, dkny169 wrote:
> > Unfortunately I cannot get to the docs, unless the same docs are
> > stored under help.start()
>
> Please explain what the problem/error is. Note that you have to load
> a package in order to use ?/help() on its methods, e.g.
>
> library("FIRMAGene");
> ?FIRMAGene
>
> If you don't load it, you get something like:
>
> > ?FIRMAGene
>
> No documentation for 'FIRMAGene' in specified packages and libraries:
> you could try '??FIRMAGene'
>
> The help is the same regardless if you access it via ?/help() or
> help.start(). So, yes, you'll find the same information if you do
> help.start() -> Packages -> FIRMAGene -> FIRMAGene
>
> /Henrik
>
>
>
> > I used following parameters:
> >>plm <- RmaPlm(csNU)
> >> plm
> > [1] "RmaPlm: 0x22388540"
> >>cls<-gsub("TisMap_","",gsub("_0(1-3)_v1_WTGene1","",getNames(cs)))
> >>cls
> > [1] "P.L_10" "P.L_11" "P.L_12" "P.L_14" "P.L_15" "P.L_16" "P.L_2"
> > "P.L_3"
> > [9] "P.L_4" "P.L_5" "P.L_6" "P.L_7" "P.L_8" "P.L_9"
>
> > I am not sure what is supposed to be stored in cls and u.
> > I’m a bit confused however, with what the whole “unique cdf set” is
> > for and how plm is working. Can I save the plm data into a txt file?
> > Many thanks for your help.
> > I really appreciate it.
> > Daniela
>
> > On Mar 16, 4:57 pm, Mark Robinson wrote:
> >> Hi Daniela.
>
> >> You haven't told us what inputs you've used for 'plm' and 'cls' ...
> >> and what is stored in 'u'?
>
> >> Have you read the docs at:
>
> >> ?FIRMAGene
>
> >> Cheers,
> >> Mark
>
> >> On 14-Mar-10, at 10:21 AM, dkny169 wrote:
>
> >> > Hello,
> >> > I have a question regarding FIRMAGene. Executing the FIRMAGene
> >> > command I get the following error:
> >> >> fg<-FIRMAGene(plm, idsToUse=u, cls=cls)
> >> > Gathering/calculating residuals.
> >> > Reading units.
> >> > Error in if (any(units < 1)) stop("Argument 'units' contains non-
> >> > positive indices.") :
> >> > missing value where TRUE/FALSE needed
>
> >> > The commands used right before are:
>
> >> >> monetaffx<-read.csv("MoEx-1_0-st-v1.na29.mm9.transcript.csv",
> >> >> sep=",",skip=20, header=TRUE,comment.char="",stringsAsFactors=FALSE)
> >> >> probetab<-read.table("MoEx-1_0-st-v1.na29.mm9.probeset.csv",
> >> >> sep="\t", header=TRUE, comment.char="", stringsAsFactors=FALSE)
> >> >> u<-which(getUnitNames(cdf) %in% monetaffx$probeset_id [monetaffx
> >> >> $category =="main" & monetaffx$total_probes >7 & monetaffx
> >> >> $total_probes <200])
>
> >> > I'm not sure what these commands do and how they need to be
> >> > changed to accommodate my own data:
>
> >> > cls <- gsub("TisMap_","",gsub("_0[1-3]_v1_WTGene1","",getNames(cs)))
>
> >> > Many thanks,
> >> > Daniela
>
> >> > --
> >> > When reporting problems on aroma.affymetrix, make sure 1) to run the
> >> > latest version of the package, 2) to report the output of
> >> > sessionInfo() and traceback(), and 3) to post a complete code example.
>
> >> > You received this message because you are subscribed to the Google
> >> > Groups "aroma.affymetrix" group.
> >> > To post to this group, send email to aroma-affymetrix@googlegroups.com
> >> > To unsubscribe from this group, send email to
> >> > aroma-affymetrix-unsubscr...@googlegroups.com
> >> > For more options, visit this group
> >> > athttp://groups.google.com/group/aroma-affymetrix?hl=en
>
> >> --
> >> Mark Robinson, PhD (Melb)
> >> Epigenetics Laboratory, Garvan
> >> Bioinformatics Division, WEHI
> >> e: m.robin...@garvan.org.au
> >> e: mrobin...@wehi.edu.au
> >> p: +61 (0)3 9345 2628
> >> f: +61 (0)3 9347 0852
> >> --
>
> >> __
> >> The information in this email is confidential and intended solely for the
> >> addressee.
> >> You must not disclose, forward, print or use it without the permission of
> >> the sender.
> >> __
>
> > --
> > When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> > version of the package, 2) to report the output of sessionInfo() and
> > traceback(), and 3) to post a complete code example.
>
> > You received this message because you are subscribed to the Google Groups
> > "aroma.affymetrix" group.
> > To post to this group, send email to aroma-affymetrix@googlegroups.com
> > To unsubscribe from this group, send email to
> > aroma-affymetrix-unsubscr...@googlegroups.com
> > For more options, visit this group
> > athttp://groups.google.com/group/aroma-affymetrix?hl=en
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a com
Re: [aroma.affymetrix] Re: FIRMAGene command
Hi.
On Thu, Mar 18, 2010 at 6:47 PM, dkny169 wrote:
> Unfortunately I cannot get to the docs, unless the same docs are
> stored under help.start()
Please explain what the problem/error is. Note that you have to load
a package in order to use ?/help() on its methods, e.g.
library("FIRMAGene");
?FIRMAGene
If you don't load it, you get something like:
> ?FIRMAGene
No documentation for 'FIRMAGene' in specified packages and libraries:
you could try '??FIRMAGene'
The help is the same regardless if you access it via ?/help() or
help.start(). So, yes, you'll find the same information if you do
help.start() -> Packages -> FIRMAGene -> FIRMAGene
/Henrik
>
> I used following parameters:
>>plm <- RmaPlm(csNU)
>> plm
> [1] "RmaPlm: 0x22388540"
>>cls<-gsub("TisMap_","",gsub("_0(1-3)_v1_WTGene1","",getNames(cs)))
>>cls
> [1] "P.L_10" "P.L_11" "P.L_12" "P.L_14" "P.L_15" "P.L_16" "P.L_2"
> "P.L_3"
> [9] "P.L_4" "P.L_5" "P.L_6" "P.L_7" "P.L_8" "P.L_9"
>
> I am not sure what is supposed to be stored in cls and u.
> I’m a bit confused however, with what the whole “unique cdf set” is
> for and how plm is working. Can I save the plm data into a txt file?
> Many thanks for your help.
> I really appreciate it.
> Daniela
>
>
> On Mar 16, 4:57 pm, Mark Robinson wrote:
>> Hi Daniela.
>>
>> You haven't told us what inputs you've used for 'plm' and 'cls' ...
>> and what is stored in 'u'?
>>
>> Have you read the docs at:
>>
>> ?FIRMAGene
>>
>> Cheers,
>> Mark
>>
>> On 14-Mar-10, at 10:21 AM, dkny169 wrote:
>>
>>
>>
>> > Hello,
>> > I have a question regarding FIRMAGene. Executing the FIRMAGene
>> > command I get the following error:
>> >> fg<-FIRMAGene(plm, idsToUse=u, cls=cls)
>> > Gathering/calculating residuals.
>> > Reading units.
>> > Error in if (any(units < 1)) stop("Argument 'units' contains non-
>> > positive indices.") :
>> > missing value where TRUE/FALSE needed
>>
>> > The commands used right before are:
>>
>> >> monetaffx<-read.csv("MoEx-1_0-st-v1.na29.mm9.transcript.csv",
>> >> sep=",",skip=20, header=TRUE,comment.char="",stringsAsFactors=FALSE)
>> >> probetab<-read.table("MoEx-1_0-st-v1.na29.mm9.probeset.csv",
>> >> sep="\t", header=TRUE, comment.char="", stringsAsFactors=FALSE)
>> >> u<-which(getUnitNames(cdf) %in% monetaffx$probeset_id [monetaffx
>> >> $category =="main" & monetaffx$total_probes >7 & monetaffx
>> >> $total_probes <200])
>>
>> > I'm not sure what these commands do and how they need to be
>> > changed to accommodate my own data:
>>
>> > cls <- gsub("TisMap_","",gsub("_0[1-3]_v1_WTGene1","",getNames(cs)))
>>
>> > Many thanks,
>> > Daniela
>>
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> > latest version of the package, 2) to report the output of
>> > sessionInfo() and traceback(), and 3) to post a complete code example.
>>
>> > You received this message because you are subscribed to the Google
>> > Groups "aroma.affymetrix" group.
>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> > To unsubscribe from this group, send email to
>> > aroma-affymetrix-unsubscr...@googlegroups.com
>> > For more options, visit this group
>> > athttp://groups.google.com/group/aroma-affymetrix?hl=en
>>
>> --
>> Mark Robinson, PhD (Melb)
>> Epigenetics Laboratory, Garvan
>> Bioinformatics Division, WEHI
>> e: m.robin...@garvan.org.au
>> e: mrobin...@wehi.edu.au
>> p: +61 (0)3 9345 2628
>> f: +61 (0)3 9347 0852
>> --
>>
>> __
>> The information in this email is confidential and intended solely for the
>> addressee.
>> You must not disclose, forward, print or use it without the permission of
>> the sender.
>> __
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe from this group, send email to
> aroma-affymetrix-unsubscr...@googlegroups.com
> For more options, visit this group at
> http://groups.google.com/group/aroma-affymetrix?hl=en
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
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[aroma.affymetrix] Re: FIRMAGene command
Unfortunately I cannot get to the docs, unless the same docs are
stored under help.start()
I used following parameters:
>plm <- RmaPlm(csNU)
> plm
[1] "RmaPlm: 0x22388540"
>cls<-gsub("TisMap_","",gsub("_0(1-3)_v1_WTGene1","",getNames(cs)))
>cls
[1] "P.L_10" "P.L_11" "P.L_12" "P.L_14" "P.L_15" "P.L_16" "P.L_2"
"P.L_3"
[9] "P.L_4" "P.L_5" "P.L_6" "P.L_7" "P.L_8" "P.L_9"
I am not sure what is supposed to be stored in cls and u.
I’m a bit confused however, with what the whole “unique cdf set” is
for and how plm is working. Can I save the plm data into a txt file?
Many thanks for your help.
I really appreciate it.
Daniela
On Mar 16, 4:57 pm, Mark Robinson wrote:
> Hi Daniela.
>
> You haven't told us what inputs you've used for 'plm' and 'cls' ...
> and what is stored in 'u'?
>
> Have you read the docs at:
>
> ?FIRMAGene
>
> Cheers,
> Mark
>
> On 14-Mar-10, at 10:21 AM, dkny169 wrote:
>
>
>
> > Hello,
> > I have a question regarding FIRMAGene. Executing the FIRMAGene
> > command I get the following error:
> >> fg<-FIRMAGene(plm, idsToUse=u, cls=cls)
> > Gathering/calculating residuals.
> > Reading units.
> > Error in if (any(units < 1)) stop("Argument 'units' contains non-
> > positive indices.") :
> > missing value where TRUE/FALSE needed
>
> > The commands used right before are:
>
> >> monetaffx<-read.csv("MoEx-1_0-st-v1.na29.mm9.transcript.csv",
> >> sep=",",skip=20, header=TRUE,comment.char="",stringsAsFactors=FALSE)
> >> probetab<-read.table("MoEx-1_0-st-v1.na29.mm9.probeset.csv",
> >> sep="\t", header=TRUE, comment.char="", stringsAsFactors=FALSE)
> >> u<-which(getUnitNames(cdf) %in% monetaffx$probeset_id [monetaffx
> >> $category =="main" & monetaffx$total_probes >7 & monetaffx
> >> $total_probes <200])
>
> > I'm not sure what these commands do and how they need to be
> > changed to accommodate my own data:
>
> > cls <- gsub("TisMap_","",gsub("_0[1-3]_v1_WTGene1","",getNames(cs)))
>
> > Many thanks,
> > Daniela
>
> > --
> > When reporting problems on aroma.affymetrix, make sure 1) to run the
> > latest version of the package, 2) to report the output of
> > sessionInfo() and traceback(), and 3) to post a complete code example.
>
> > You received this message because you are subscribed to the Google
> > Groups "aroma.affymetrix" group.
> > To post to this group, send email to aroma-affymetrix@googlegroups.com
> > To unsubscribe from this group, send email to
> > aroma-affymetrix-unsubscr...@googlegroups.com
> > For more options, visit this group
> > athttp://groups.google.com/group/aroma-affymetrix?hl=en
>
> --
> Mark Robinson, PhD (Melb)
> Epigenetics Laboratory, Garvan
> Bioinformatics Division, WEHI
> e: m.robin...@garvan.org.au
> e: mrobin...@wehi.edu.au
> p: +61 (0)3 9345 2628
> f: +61 (0)3 9347 0852
> --
>
> __
> The information in this email is confidential and intended solely for the
> addressee.
> You must not disclose, forward, print or use it without the permission of the
> sender.
> __
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
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