HELLO! I am sorting out genes from micro array data by using R. i have faced an error during running commands and stuck on it . please anyone help me to solve it.
groups = pData(phenoData(gse17906dat[[1]]))$source_name_ch1
groups=as.character(groups)
groups[groups=="normal prostate"]="control"
groups[groups=="cancer prostate"]="disease"
groups[groups=="normal bladder"]="normal"
groups[groups=="cancer bladder"]="cancerous"
groups[groups=="prostate tumor Gleason 3"]="tumor"
f = factor(groups, levels=c("disease","control","normal","cancerous","tumor"))
design_gse17906 = model.matrix(~0+f)
colnames(design_gse17906) = levels(f)
cont.matrix = makeContrasts(disease-control, levels=design_gse17906)
fit = lmFit(gse17906eset, design_gse17906)
fit2= contrasts.fit(fit, cont.matrix)
fit2 = eBayes(fit2)
fit2$genes$Symbol = getSYMBOL(fit2$genes$ID, "hgu133plus2")
Error in lookUp(x, data, "SYMBOL") : No keys provided
how to remove this error!
