[BioC] Problom in performing Gene Set Test using KEGG
Aditya [guest]
guest at bioconductor.org
Sun Jun 22 14:41:50 CEST 2014
i am new to Bioconductor and I want to analyze dataset GSE23343, which contain 17 samples (7 normal and 10 T2D)
i am following http://koti.mbnet.fi/tuimala/oppaat/r2.pdf book, on page number 102 gene set test using KEGG is there.
kindly let me know the problom in my code.
why i am encountering this problom ?
Error in .getNull(null, data, n, model) :
argument "null" could not be coerced into a matrix
-- output of sessionInfo():
> dat<-ReadAffy()
> dat
AffyBatch object
size of arrays=1164x1164 features (14 kb)
cdf=HG-U133_Plus_2 (54675 affyids)
number of samples=17
number of genes=54675
annotation=hgu133plus2
notes=
> dat2<-rma(dat)
Background correcting
Normalizing
Calculating Expression
> dat.m<-exprs(dat2)
> library(hgu133plus2.db)
Loading required package: org.Hs.eg.db
Loading required package: DBI
> pathway2probe<-get("hgu133plus2PATH2PROBE")
> kegg<-as.list(pathway2probe)
> library(globaltest)
> groups<-c(0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1)
> test.kegg<-gt(as.matrix(dat.m), groups, kegg)
Error in .getNull(null, data, n, model) :
argument "null" could not be coerced into a matrix
--
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