Question: Error in R commands
0
gravatar for 786
3.1 years ago by
78650
78650 wrote:

I'm working with GSE12643 and want to extract differentially expressed gene.Can any one help me in removing the error...

study4 = "GSE12643" 
gse12643dat = getGEO('GSE12643') 
gse12643raw= getGEOSuppFiles(study4)  
tarfile <- grep("\\.tar$", rownames(gse12643raw), value = TRUE) 
untar(tarfile, exdir="study4") 
celFiles <- unlist(list.files("study4", pattern = "\\.CEL.gz", full.names = TRUE)) 
gse12643preset = ReadAffy(filenames = celFiles) 
rmaData = rma(gse12643preset) 
gse12643eset= exprs(rmaData)  
groups = pData(phenoData(gse12643dat[[1]]))$source_name_ch1 
groups=as.character(groups) 
groups[groups=="myotubes from control subject"]="Control" 
groups[groups=="myotubes from type 2 diabetes subject"]="T2D" 
f = factor(groups, levels=c("Control","T2D")) 
design_gse12643 = model.matrix(~0+f) 
colnames(design_gse12643) = levels(f) 
cont.matrix = makeContrasts(T2D-Control, levels=design_gse12643) 
fit = lmFit(gse12643eset, design_gse12643)
 fit2 = contrasts.fit(fit, cont.matrix) 
fit2 = eBayes(fit2)  
fit2$genes$Symbol = getSYMBOL(fit2$genes$ID, "hgu95av2") 
fit2$genes$GeneName = unlist(mget(fit$genes$ID, hgu95av2GENENAME))  
results = topTable(fit2, adjust ="BH", number = nrow(gse12643eset))

Error is in last command i.e., results = topTable(fit2, adjust ="BH", number = nrow(gse12643eset)) EEROR:

Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x),  : 
  attempt to set an attribute on NULL

Please help me out.

limm affy geoquery R • 990 views
ADD COMMENTlink written 3.1 years ago by 78650
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