Question: Error in R commands
gravatar for 786
4.1 years ago by
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[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 =, 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 • 1.2k views
ADD COMMENTlink written 4.1 years ago by 78650
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1174 users visited in the last hour