Question: Error in lookUp(x, data, "SYMBOL") : No keys provided
gravatar for muhammadzubair777
4.2 years ago by
muhammadzubair77710 wrote:

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[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=, 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!

microarray data bioconductor R • 1.3k views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by muhammadzubair77710
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