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bhklab / genefu

R package providing various functions relevant for gene expression analysis with emphasis on breast cancer.
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oncotypedx risk score NA #12

Closed IL2liu closed 5 years ago

IL2liu commented 5 years ago

I am trying to use the powerful R package "genefu"to compute the risk score of my dataset. Following the user's guide and vignettes provided by bioconductor platform, however,I just get the all reulsts NA. my R code is as following:

ddata has been prepared as a Matrix of RNA-seq gene expressions with samples in rows and probes in columns

dnanot has been prepared as Matrix of annotations, first colums:gene symbol(colname probe), second: gene.symbol, third, EntrezGene.ID

rs.exp<-oncotypedx(data=ddata,annot=dannot,mapping=TRUE) table(rs.exp$score)

< table of extent 0 > the result be returned, that is, all score are NA.

IL2liu commented 5 years ago

Following the suggestion of Pro. Benjamin Haibe-Kains, my issue was solved.

rownames(dannot) <- as.character(dannot[ , "probe”]) rs.nkis <- oncotypedx(data=ddata,annot=dannot, do.mapping=TRUE)

I found that the Matrix of annotations should have proper rownames. Just like this: probe Gene.Symbol EntrezGene.ID LOC100506869 LOC100506869 LOC100506869 100506869 LOC102724601 LOC102724601 LOC102724601 102724601 CHMP1B CHMP1B CHMP1B 57132