[BioC] problem with function rma
Martin Morgan
mtmorgan at fhcrc.org
Wed May 30 04:26:44 CEST 2007
Hi Juan --
"Juan Lin" <julin at aecom.yu.edu> writes:
> Hello Bioconductorers,
>
> I am working with 12 affy rat2302 chips recently. It was OK when I tried to
> read my cel files into R:
>
>> RatData<-ReadAffy()
>> list.celfiles()
> [1] "Rat 16hrs-1-2113.CEL" "Rat 16hrs-2-2114.CEL" "Rat 16hrs-3-2115.CEL"
> [4] "Rat 30hrs-1-2116.CEL" "Rat 30hrs-2-2117.CEL" "Rat 30hrs-3-2118.CEL"
> [7] "Rat 4hrs-1-2110.CEL" "Rat 4hrs-2-2111.CEL" "Rat 4hrs-3-2112.CEL"
> [10] "Rat Normal-1-2107.CEL" "Rat Normal-2-2108.CEL" "Rat Normal-3-2109.CEL"
>
probably sampleNames(RatData) returns the same vector as
list.celfiles() ?
>> phenoData(RatData) <- read.phenoData("phenoData.txt",header=T)
probably validObject(RatData) would fail here -- you're allowed to
assign inconsistent names, in the hopes that you're going to make them
consistent again in the next line...
>> show(pData(phenoData(RatData)))
> ID time replicate
> Rat Normal-1-2107.CEL 2107 0 1
> Rat Normal-2-2108.CEL 2108 0 2
> Rat Normal-3-2109.CEL 2109 0 3
> Rat 4hrs-1-2110.CEL 2110 4 1
> Rat 4hrs-2-2111.CEL 2111 4 2
> Rat 4hrs-3-2112.CEL 2112 4 3
> Rat 16hrs-1-2113.CEL 2113 16 1
> Rat 16hrs-2-2114.CEL 2114 16 2
> Rat 16hrs-3-2115.CEL 2115 16 3
> Rat 30hrs-1-2116.CEL 2116 30 1
> Rat 30hrs-2-2117.CEL 2117 30 2
> Rat 30hrs-3-2118.CEL 2118 30 3
Notice that the cel files and phenoData names are not in the same
order-- you've associated the wrong phenoData with your cel files. One
thing you could do is
pd <- read.phenoData("phenoData.txt",header=TRUE)
pd <- pd[sampleNames(RatData),] # re-order; check carefully
phenoData(RatData) <- pd
validObject(RatData)
> However, when I was going to do normalization, I got an error message as
> following:
>
>> esetRat <- rma(RatData)
> Background correcting
> Normalizing
> Calculating Expression
> Error in validObject(.Object) : invalid class "exprSet" object: sampleNames
> different from names of phenoData rows
>
> Can anyboday give me a clue on how to solve this problem?
>
> BTW. my sessionInfor is as following:
R 2.5.0 is out, and so are the 1.14.x series of affy and Biobase. One
thing that will change when you update is that affy will produce an
eSet-based AffyBatch, which is slightly different:
1) update any old instances with rat <- updateObject(RatData)
2) use read.AnnotatedDataFrame rather than read.phenoData.
Hope that helps,
Martin
>> sessionInfo()
> R version 2.4.0 (2006-10-03)
> 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] "splines" "tools" "methods" "stats" "graphics" "grDevices"
> [7] "utils" "datasets" "base"
>
> other attached packages:
> rat2302cdf affyQCReport simpleaffy genefilter survival
> affy
> "1.14.0" "1.12.0" "2.8.0" "1.12.0" "2.31"
> "1.12.1"
> affyio Biobase
> "1.2.0" "1.12.2"
>
> Thanks a lot!
> Juan
>
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--
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org
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