[BioC] Data Frame Error in Affycomp

McGee, Monnie mmcgee at mail.smu.edu
Mon Dec 19 03:55:56 CET 2005


Dear R-Help,

I am trying to use affycomp to do some assessments of a new method with the spikein data using the Hgu-133 chip.   Just to make sure that the problem was in affycomp in not in my method, I used the affy package version of RMA to do create the CSV file.  Here's what I did:

> spike133 <- ReadAffy()
> spike133
AffyBatch object
size of arrays=712x712 features (166358 kb)
cdf=HG-U133A_tag (22300 affyids)
number of samples=42
number of genes=22300
annotation=hgu133atag
> bgcrma <- expresso(spike133,bgcorrect.method="rma",normalize.method="quantiles",pmcorrect.method="pmonly",summary.method="medianpolish")
background correction: rma 
normalization: quantiles 
PM/MM correction : pmonly 
expression values: medianpolish 
background correcting...done.
normalizing...done.
22300 ids to be processed
## Transform back to original scale, as per directions on Affycomp website:
> eset <- exprs(bgcrma)
> log.bgcrma <- bgcrma
> exprs(bgcrma) <- 2^eset
> new.eset <- exprs(bgcrma)
> write.table(data.frame(new.eset,check.names=FALSE),"rma-133.csv",sep=",",col.names=NA,quote=FALSE)
> library(affycomp)
> read.spikein("rma-133.csv")
Error in "[.data.frame"(s, , rownames(pData(pd))) : 
	undefined columns selected

The funny thing is that when I follow the same procedures with the spikein data on the HGU-95 chip, I have no problem reading the data into affycomp.

FYI - Here the version of R I am using:
R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.2.0  (2005-10-06 r35749)
ISBN 3-900051-07-0
I am running R on Mac OS X (Tiger) using R-Aqua 2.2.1, r-app 1.13.
I had a student run the same scenario on a PC and he received the same result.

Thank you for your help,
Monnie

Monnie McGee, Ph.D.
Assistant Professor
Department of Statistical Science
Southern Methodist University
Ph: 214-768-2462
Fax: 214-768-4035



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