[BioC] SimpleAffy - problem with pairwise.comparison(), can't construct PairComp object
Crispin Miller
CMiller at picr.man.ac.uk
Mon Feb 26 18:11:22 CET 2007
Hi Peter,
What's your sessionInfo()? I suspect you might need to upgrade to the
latest version of the package ...
Crispin
-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Peter
Lambert
Sent: 24 February 2007 21:24
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] SimpleAffy - problem with pairwise.comparison(),can't
construct PairComp object
Hi,
I've been using some of the SimpleAffy functions to analyze some GEO
experiments. I have the following exprSet:
> Data
Expression Set (exprSet) with
22690 genes
8 samples
phenoData object with 1 variables and 8 cases
varLabels
tissue: read from file
> pData(Data)
tissue
GSM73331 control
GSM73332 control
GSM73333 control
GSM73334 control
GSM73335 dystrophic
GSM73336 dystrophic
GSM73337 dystrophic
GSM73338 dystrophic
> res<-pairwise.comparison(Data,"tissue",c("control","dystrophic"),logge
> d=F)
Error in validObject(.Object) : invalid class "PairComp" object: invalid
object for slot "pData" in class "PairComp": got class "factor", should
be or extend class "data.frame"
The problem seems to be in the get.fold.change.and.t.test() function,
where the pData object comes out as a factor for some reason, and thus
the new PairComp object can't be constructed.
I don't have this problem when I read in cel files and phenodata using
ReadAffy, and then use rma() to construct an exprSet.
For the GEO data, I'm constructing the exprSet using the following:
p<-read.table(file=GSE3252_series_matrix.txt,header=T,row.names=1,
comment.char="!")
pheno<-read.phenoData("pdata.txt",sep="\t",header=T,row.names=1)
Data<-new('exprSet',exprs=as.matrix(p),phenoData=pheno)
I would appreciate any insight or help.
Thanks,
Peter Lambert
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