Error in lookUp(x, data, "SYMBOL") : No keys provided
0
1
Entering edit mode
7.8 years ago

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!

R BIOCONDUCTOR MICROARRAY DATA • 1.9k views
ADD COMMENT

Login before adding your answer.

Traffic: 1077 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6