I am using justRMA to analyze Affy rat2302 chips. I do have installed
on
my system the alternative MBNI cdf package but do not want to use it
in
this case. For some reason, just.rma and justRMA are using the MBNI
cdf
as the default cdf file and using the parameter "cdfname = 'rat2302'"
does not work to over-ride. Below is my code and sessionInfo. Note
that
I am using the devel versions or R and BioC with all latest package
updates installed.
Thanks, Mark
> affy.object.preprocessed$eSet <-just.rma(filenames=list.celfiles(),
phenoData = read.pData.ordered.func("pdata.3.txt"))
Background correcting
Normalizing
Calculating Expression
> affy.object.preprocessed$eSet
Expression Set (exprSet) with
10255 genes
30 samples
phenoData object with 2 variables and 30 cases
varLabels
Condition: read from file
Treatment: read from file
> annotation(affy.object.preprocessed$eSet)
[1] "rn230rnentrezg6"
> sessionInfo()
Version 2.3.0 Under development (unstable) (2006-01-01 r36947)
i386-pc-mingw32
attached base packages:
[1] "splines" "tools" "methods" "stats" "graphics"
"grDevices" "utils" "datasets" "base"
other attached packages:
rn230rnentrezg6cdf affycoretools GOstats
multtest genefilter survival xtable
RBGL
"6.0.0" "1.3.1" "1.5.4"
"1.8.0" "1.9.2" "2.20" "1.3-0"
"1.7.7"
annotate GO graph
Ruuid cluster limma affy
Biobase
"1.9.2" "1.6.5" "1.9.9"
"1.9.0" "1.10.2" "2.4.9" "1.9.7"
"1.9.6"
>
Mark W. Kimpel MD
Hi Mark,
Kimpel, Mark William wrote:
> I am using justRMA to analyze Affy rat2302 chips. I do have
installed on
> my system the alternative MBNI cdf package but do not want to use it
in
> this case. For some reason, just.rma and justRMA are using the MBNI
cdf
> as the default cdf file and using the parameter "cdfname =
'rat2302'"
> does not work to over-ride. Below is my code and sessionInfo. Note
that
> I am using the devel versions or R and BioC with all latest package
> updates installed.
>
> Thanks, Mark
>
>
>>affy.object.preprocessed$eSet <-just.rma(filenames=list.celfiles(),
>
> phenoData = read.pData.ordered.func("pdata.3.txt"))
This is sort of an unusual thing to do. Why are you putting your
exprSet
into a list? Also, what does read.pData.ordered.func() do? I can't
find
this function.
Anyway, I can't reproduce what you are seeing:
> eset <- just.rma(filenames=list.celfiles())
Background correcting
Normalizing
Calculating Expression
Warning message:
Incompatible phenoData object. Created a new one.
in: just.rma(filenames = list.celfiles())
> annotation(eset)
[1] "mouse4302"
> eset <- just.rma(filenames=list.celfiles(),
cdfname="mm430mm3enst6")
Attaching package: 'mm430mm3enst6cdf'
The following object(s) are masked from package:mouse4302cdf
:
i2xy xy2i
Background correcting
Normalizing
Calculating Expression
Warning message:
Incompatible phenoData object. Created a new one.
in: just.rma(filenames = list.celfiles(), cdfname = "mm430mm3enst6")
> annotation(eset)
[1] "mm430mm3enst6"
> eset <- just.rma(filenames=list.celfiles(), cdfname="mouse4302")
Background correcting
Normalizing
Calculating Expression
Warning message:
Incompatible phenoData object. Created a new one.
in: just.rma(filenames = list.celfiles(), cdfname = "mouse4302")
> annotation(eset)
[1] "mouse4302"
> sessionInfo()
Version 2.3.0 Under development (unstable) (2006-01-01 r36947)
i386-pc-mingw32
attached base packages:
[1] "splines" "tools" "methods" "stats" "graphics"
"grDevices" "utils"
[8] "datasets" "base"
other attached packages:
mm430mm3enst6cdf mouse4302cdf affycoretools GOstats
multtest
"6.0.0" "1.10.0" "1.3.1" "1.5.4"
"1.9.3"
genefilter survival xtable RBGL
annotate
"1.9.1" "2.20" "1.3-0" "1.7.5"
"1.9.2"
GO graph Ruuid cluster
limma
"1.11.0" "1.9.4" "1.9.0" "1.10.2"
"2.4.7"
affy Biobase
"1.9.7" "1.9.4"
Best,
Jim
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
Jim,
The problem appears to be a corrupt data file as I cannot reproduce
the
error with other datasets.
To answer your other questions... I put the eset into a list with
another slot reserved for annotation information. That way I only have
to build the annotation once and then store it in a database with the
eset. Maybe a bit odd, but I'm not a trained programmer and it works
for
me.
The read.pData.ordered.func function is something I wrote to make sure
that the proper phenotype information was correctly assigned to
samples.
Not long ago I needed to sort my pdata file by phenotype to check
something and forgot to resort it by sampleName before saving it.
After
getting some puzzling analysis results I discovered that
read.phenoData
does not match sampleNames with CEL file names (in my case one and the
same) so I wrote this function to do that. I will share the code,
simple
as it is, in case this is beneficial to anyone else (see below).
Thanks,
Mark
read.pData.ordered.func<-function(pdata.file)
{
pD <- read.phenoData(filename = pdata.file, sep = "\t", header=TRUE,
row.names=1)
cel.files<-list.celfiles()
for (i in 1:length(cel.files))
{
cel.files[i]<-substr(x=cel.files[i], start=1,
stop=(nchar(cel.files[i])-4))
}
pos<-match(cel.files, rownames(pD at pData))
pD<-pD[pos]
pD
}
