[BioC] problem with function rma

[Juan Lin]

Martin,

It works after I change the order of phenoData names! And I will update both
R and bioconductor today.

Thanks a lot for your help!

Juan

-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
Sent: Tuesday, May 29, 2007 9:27 PM
To: Juan Lin
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] problem with function rma


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