[BioC] Problems with affycomp - quantile.default

[James W. MacDonald]

Are you sure you have the correct phenoData? What do you get from

colnames(pData(eset))?

You should get this:

 > colnames(pData(eset))
  [1] "37777_at" "684_at"   "1597_at"  "38734_at" "39058_at" "36311_at"
  [7] "36889_at" "1024_at"  "36202_at" "36085_at" "40322_at" "407_at"
[13] "1091_at"  "1708_at"  "33818_at" "546_at"

If you don't, you have the incorrect phenoData, and you should use

pd <- as(data(spikein.phenodata), "AnnotatedDataFrame")

Best,

Jim



Markus Schmidberger wrote:
> 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
>>>
> 
> 

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