Hello,

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 &nbsp;&nbsp;&nbsp;&nbsp; EntrezGene.ID &nbsp;&nbsp;&nbsp;&nbsp; Gene.ID &nbsp;&nbsp;&nbsp;&nbsp; Gene.Symbol

Data refers to the input file, which is of the format -

>Gene.Symbol &nbsp;&nbsp;&nbsp;&nbsp; Sample1 &nbsp;&nbsp;&nbsp;&nbsp; SAMPLE2 &nbsp;&nbsp; ... &nbsp;&nbsp; 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 `Gene.Symbol` and `probe` in the data file, but both give the same error.

Edit: Should my data file also contain the `EntrezGene.ID` column?

Thank you.
Hi vinayjrao,

I think the problem is with the `data` matrix; `molecular.subtyping` fuction expects a matrix of samples(rows) x genes(cols). As I can see above your data matrix is genes x samples, right? Try transposing the matrix. 

From the genefu vignette for do.mapping: `TRUE if the mapping through Entrez Gene ids must be performed (in case of ambiguities, the most variant probe is kept for each gene)`