I'm analyzing TCGA breast cancer data to classify the samples into their respective subtypes, ad then to check if the genes of our study have a subtype specific pattern of expression. To do this, I was suggested to use
genefu. At the step of classifying the subtypes -
PAM50Base <- molecular.subtyping(sbt.model = "pam50",data=data, annot=annot,do.mapping=F)
I get an error -
Error in intrinsic.cluster.predict(sbt.model = pam50.robust, data = data, :
no probe in common -> annot or mapping parameters are necessary for the mapping process!
In the command, annot is the file used for annotation and is of the format -
probe EntrezGene.ID Gene.ID Gene.Symbol
Data refers to the input file, which is of the format -
Gene.Symbol Sample1 SAMPLE2 ... Sample 1092
Both files are tab delimited. I want to know if anyone has done this before, and if the file formatting is correct?
P.S. I have tried using the
probe in the data file, but both give the same error.
Edit: Should my data file also contain the