Hello to all,

I think there is a problem with a certain call of justRMA (see below); it mixes the sample names of pData but keeps the annotation the same, effectively miss labeling samples without returning a single error or warning. 

> phenoData <- read.AnnotatedDataFrame(paste(prodir, "sample_pheno.txt", sep="/"), sep="\t")
> head(pData(phenoData))
                              Line        Resistance Media Condition
28_MGH006_neg.CEL           MGH006             Naive   D10      Cont
30_MGH006_criz.CEL          MGH006             Naive  D10   Criz 300
21_MGH010_neg.CEL           MGH010              Criz  R10       Cont
15_MGH010_Criz.CEL          MGH010              Criz  R10   Criz 300
9_MGH021_neg.CEL   MGH021-2 (pool) Criz (1269 et al)   A10      Cont
4_MGH021_LDK.CEL   MGH021-2 (pool) Criz (1269 et al)   A10   LDK 300


> eset <- justRMA(phenoData=phenoData, celfile.path=celdir)
> head(pData(eset))
                                   Line        Resistance Media Condition
10_MGH025_neg.CEL                MGH006             Naive   D10      Cont
11_MGH022_neg.CEL                MGH006             Naive  D10   Criz 300
12_MGH_049_criz.CEL              MGH010              Criz  R10       Cont
13_MGH025_criz_0530.CEL          MGH010              Criz  R10   Criz 300
14_MGH025_LDK.CEL       MGH021-2 (pool) Criz (1269 et al)   A10      Cont
15_MGH010_Criz.CEL      MGH021-2 (pool) Criz (1269 et al)   A10   LDK 300

## IN CONTRAST, THIS WORKS CORRECTLY:
eset <- justRMA(phenoData=paste(prodir, "sample_pheno.txt", sep="/"), celfile.path=celdir) 


I hope people appreciate this might lead to completely wrong results, and that it should be addressed in some way by the authors ?

Best regards, 

Arnaud Amzallag, PhD
Center for Cancer Research, Massachusetts General Hospital/Harvard Medical School

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] hgu133plus2cdf_2.12.0 AnnotationDbi_1.22.6  affy_1.38.1          
[4] Biobase_2.20.1        BiocGenerics_0.6.0    rj_1.1.3-1           

loaded via a namespace (and not attached):
 [1] BiocInstaller_1.10.4  DBI_0.2-7             IRanges_1.18.4       
 [4] RSQLite_0.11.4        affyio_1.28.0         preprocessCore_1.22.0
 [7] rj.gd_1.1.3-1         stats4_3.0.1          tools_3.0.1          
[10] zlibbioc_1.6.0       
 
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