On 17/05/15 10:32, Lyle Warren wrote:
Hi,
I have multiple files that I want to compare in R. They contain SNP data
with genotype in the 4th column, which is what I want to compare.
Is there any easy way to do this?
Yes. Learn to use R.
cheers,
Rolf Turner
--
Technical Editor ANZJS
Angela,
My guess is that your data are not balanced.
That could be due to a typo in one of the factors, or it could be that
you actually have different numbers of observations at some of the
factor levels.
Rich
On Sun, May 17, 2015 at 12:05 PM, Angela Radulescu
angela.radule...@gmail.com wrote:
Cordial saludo
a todos
Quisiera saber si alguien me puede colaborar con dos cosillas
1) Cómo debo hacer para construir una tabla en la que las columnas salgan los
encabezados.2) He escrito un pequeño script y quiero ocultarlo para que no
quede al alcanace de los usuarios, pero desde luego que
This is a very domain-specific question (genetic data analysis), not so much a
question about how to use R, so does not seem on topic here. I also suspect
that the company 23andme may use some proprietary algorithms, so replicating
their results could be a tall order.
You might start with the
You desperately need to study [1] and the Posting Guide mentioned at the bottom
of this and every other message on this list.
[1]
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
---
OFFTOPIC! This is a statistical question, not an R question. Post on a
statistics site like stats.stackexchange.com .
However, your post suggests that you are completely out of your depth
here (0/1 responses suggest that glm modeling via logistic regression
is called for). Remote internet advice
Hi Yonas,
If this is the ca function from the package of the same name, it
looks to me as though your data set is only two dimensions and you are
requesting 3 dimensions in the output. Have you tried calling ca with
the default nd=NA?
Jim
On Mon, May 18, 2015 at 3:22 AM, Jeff Newmiller
Thanks, I think you're right. I removed the strains whose final OD was
below 0.2 since all the ones that clearly grew are above that, and
grofit produces fewer errors on the remaining 6. The error still happens
occasionally, but if I stick to 1000 bootstraps instead of 1 it's
not often. Of
Hola,
La opción en la que he pensado cuando he visto tu correo es en el paquete
compiler que permite compilar bytecode una función, con el objetivo de
acelerar su ejecución.
El problema es que cuando he ido a ver su disponibilidad en CRAN no la he
encontrado...
Te dejo la referencia de cómo se
Dears,
I have presence and absence data set (8 rows and 33 columns) and when I
want to get out of the default two dimensions command using summary(ca(mydata,
nd=3)) the following error message displyed:
Error in dimnames(phi) - list(rn, dims) :
length of 'dimnames' [2] not equal to array extent
I have the following R output from a mixed factorial ANOVA:
Error: subj
Df Sum Sq Mean Sq F value Pr(F) group
1 11.3 11.26 0.449 0.50811
singleType10.70.66 0.026 0.87220 group:singleType
1 237.5 237.53 9.484 0.00461 **Residuals28 701.3
(No response necessary)
What struck me about this post was the apparent mismatch: the OP
seemed not to have a clue where to begin. Maybe he somehow has been
assigned or chose a task for which his skills and background are
inadequate. This is not really a criticism: if someone told me to make
a
HI R user,
I was trying to reduce my independent variables before I run models. I have a
dependent variable as a present or TRUE only (no Absence or False) whereas I
have more than 20 independent variables but they are highly correlated. I was
trying to reduce the independent variables . I
Thanks Jeff, Bert!
You are right - definitely out of my skill area.. I've no found some help
on the bioconductor mailing list.
On 18 May 2015 at 03:04, Bert Gunter gunter.ber...@gene.com wrote:
(No response necessary)
What struck me about this post was the apparent mismatch: the OP
seemed
Hi,
I tried the formula
sum(psi*X[(t-1):(t-K)])
but it provides the vector of all observations. Thus, I changed K to k where
K-3 and k-1:K
This yields better results but not what I want since I should get 3 values as
K=3.
X[(t-1):(t-k)]
[1] 0.1
Warning message:
In (t - 1):(t - k) :
On 05/17/2015 01:52 PM, Lyle Warren wrote:
Thanks Jeff, Bert!
You are right - definitely out of my skill area.. I've no found some help
on the bioconductor mailing list.
I'm not sure that you've asked in the right place
https://support.bioconductor.org
see also
Thanks and sorry for being light on detail.
I have multiple files of raw human genome SNP data. Very large - the
compressed zip files are about 8mb large.
On 17 May 2015 at 20:53, John Kane jrkrid...@inbox.com wrote:
Probably but since you have not told us anything about what you are doing
Thank you all for your time..
Thank you Now its working :))
Cheers .
On Sun, May 17, 2015 at 4:34 AM, Jim Lemon drjimle...@gmail.com wrote:
Hi കുഞ്ഞായി,
It looks like you want write.table.
# as Rui Suggested
names(index_data) - paste0(V, 1:length(index_data))
Welcome to R and the R-help list.
If I am not misunderstanding you, you expect use the qcc package from within
the Rcmdr GUI.
I have never really used RCommander, though I played around with it a few years
ago, but I don't believe it can call qcc directly. I 'think' you have the
choice
Probably but since you have not told us anything about what you are doing it
is difficult to say.
You might find these links helpful
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
and http://adv-r.had.co.nz/Reproducibility.html
John Kane
Kingston ON
John Kane
Kingston ON Canada
-Original Message-
From: lyl...@gmail.com
Sent: Sun, 17 May 2015 20:56:24 +1000
To: jrkrid...@inbox.com
Subject: Re: [R] Comparing 2 different files in R
This is not an area I am going to be able to help with but we still need a lot
more information I think.
I'm trying to use the grofit package to compare growth rates between
bacterial cultures, but I've come across a couple glitches/things I
don't understand. I'm not sure if they're related to the package or to a
problem with my growth data, which is messy. Some strains don't follow
a proper
1. Very likely, you have insufficient data in some of your growth
curves to do the fits using gcv. If you remove the curves where the
bacteria didn't grow, things should work. Alternatively, there may
well be ways of expressing the model that would allow pooling across
cultures that didn't grow.
I am completely new to R and am trying to utilize its capabilities as an
alternative to Minitab. I don't have any development ability at all, but
the R Commander GUI is able to give me the functionality I need with the
exception of control charts. I have installed the qcc package but when I
load
Hi കുഞ്ഞായി,
It looks like you want write.table.
# as Rui Suggested
names(index_data) - paste0(V, 1:length(index_data))
write.table(index.table,index_table_file.txt,row.names=FALSE)
Jim
On Sun, May 17, 2015 at 4:33 AM, Rui Barradas ruipbarra...@sapo.pt wrote:
Hello,
I'm not exactly sure of
Hi R users,
I am looking for examples of software that comes with an inbuilt connector
to Rserve. The only thing I have found so far is Tableau:
http://www.simafore.com/blog/bid/120209/Integrating-Tableau-and-R-for-data-analytics-in-four-simple-steps
Please let me know if anyone knows of more
Hi,
I have multiple files that I want to compare in R. They contain SNP data
with genotype in the 4th column, which is what I want to compare.
Is there any easy way to do this?
[[alternative HTML version deleted]]
__
R-help@r-project.org
Hi,
I'm trying to replicate 23andMe's parentage test results within R, using
the 23andme raw data. Does anyone know a simple way to do this? I have read
the data with gwascat and it seems to be in there fine.
Thanks for any help you can give!
Cheers,
Lyle
[[alternative HTML version
Dear John and Greg,
As John says, even with the about 40 plugin packages that are on CRAN (the R
package archive network), the Rcmdr covers only a small fraction of what's
available in base R and the thousands of CRAN packages.
As it turns out, however, there's an Rcmdr quality-control plugin
Thanks John,
I had not realised they were on CRAN. Definately a great help.
John Kane
Kingston ON Canada
-Original Message-
From: j...@mcmaster.ca
Sent: Sun, 17 May 2015 08:15:14 -0400
To: jrkrid...@inbox.com, gjkr...@gmail.com
Subject: Re: [R] R Commander qcc
Dear John and
Thanks Ben!
On 17 May 2015 at 23:14, Ben Tupper ben.bigh...@gmail.com wrote:
Hi,
On May 17, 2015, at 6:56 AM, Lyle Warren lyl...@gmail.com wrote:
Thanks and sorry for being light on detail.
I have multiple files of raw human genome SNP data. Very large - the
compressed zip files are
Lots of questions. I'm only answering some of them, inline.
On 15/05/2015 9:04 PM, Glenn Schultz wrote:
I have an R package Bond Lab which actually supports a book Investing in MBS
using R and Open Source Computing. The Bond Lab beta is stable. I have also
created a package companion to
Hi,
On May 17, 2015, at 6:56 AM, Lyle Warren lyl...@gmail.com wrote:
Thanks and sorry for being light on detail.
I have multiple files of raw human genome SNP data. Very large - the
compressed zip files are about 8mb large.
You'll have better luck asking on the Bioconductor help list (
Hi. I have been trying to use the Rssa singular spectrum analysis library on a
dataset of 15 minute data at four (cohesive) water temperature stations in an
estuary. The stations have different missing data patterns, though I can find a
period of 2 years where all four are mostly present. There
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