[BioC] Problems with affycomp - quantile.default

[James MacDonald]

Hi Markus,

Markus Schmidberger wrote:
> Hello,
> 
> I want to do some comparison with affycomp and use the affycompII data. 
> This is my code
> 
> library(affy)
> library("affycomp")
> path <- "/Microarray/hgu95a-spikein/rawdata"
> celFile <- list.celfiles(path=path,full.names=TRUE);
> affyBatch <- ReadAffy(filenames=celFile);
> eset1 <- rma(affyBatch)
> assessFC(eset1,method.name="RMA.2")
> 
> and I get the ERROR:
> Fehler in quantile.default(m[-spikeindex], prob = probs) :
>         missing values and NaN's not allowed if 'na.rm' is FALSE

If you look at the code for assessFC(), you will see that the spikeindex 
comes from the phenoData slot of the ExpressionSet object (in particular 
the genenames column, which I assume lists the probesets that were 
spiked in). If you don't have this information in your phenoData slot, 
then assessFC() won't work, and I assume this to be true of the other 
assessXX() functions as well.

The phenoData can be accessed using data(spikein.phenodata). 
Unfortunately this is an old-style phenoData object instead of an 
AnnotatedDataFrame, so you have to update first.

pd <- data(spikein.phenodata)
pd <- as(pd, "AnnotatedDataFrame")
## you will see warnings here that I think you can ignore
affyBatch <- ReadAffy(filenames=celFile, phenoData=pd)

should get you going.

Best,

Jim


> 
> How to fix this?
> 
> R version 2.5.0 (2007-04-23)
> i686-pc-linux-gnu
> locale:
> LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "methods"   "base"    
> other attached packages:
> hgu95acdf  affycomp      affy    affyio   Biobase
>  "1.16.0"  "1.12.0"  "1.14.1"   "1.4.0"  "1.14.0"
> 
> Thanks,
> Markus
> 

-- 
James W. MacDonald, MS
Biostatistician
UMCCC cDNA and Affymetrix Core
University of Michigan
1500 E Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623