[BioC] Problems with affycomp - quantile.default

[Markus Schmidberger]

Hello,

Phenodata do not help. I changed my code to this:

library(affy)
library(affycomp)
pathRawData <- "~/Microarray/hgu95a-spikein/rawdata"
pathPhenoData <- "~/Microarray/hgu95a-spikein/spikein_pdata.txt"
celFile <- list.celfiles(path=pathRawData,full.names=TRUE);
pd<-read.AnnotatedDataFrame(filename=pathPhenoData, header=TRUE, 
row.names="filename", sep=" ")
affyBatch <- ReadAffy(filenames=celFile, phenoData=pd);
eset <- rma(affyBatch)
assessFC(eset,method.name="RMA")

and I still have the same error:
Fehler in quantile.default(m[-spikeindex], prob = probs) :
        missing values and NaN's not allowed if 'na.rm' is FALSE

(same error with the hgu133 dataset)

What I have to change?

Thanks,
Markus

James MacDonald schrieb:
> 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
>>
>


-- 
Dipl.-Tech. Math. Markus Schmidberger

Ludwig-Maximilians-Universität München
IBE - Institut für medizinische Informationsverarbeitung,
Biometrie und Epidemiologie
Marchioninistr. 15, D-81377 Muenchen
URL: http://ibe.web.med.uni-muenchen.de 
Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
Tel: +49 (089) 7095 - 4599