[BioC] justRMA using incorrect default cdf

[James W. MacDonald]

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