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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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Need for a column called "probe" in "annot" for "molecular.subtyping" and "intrinsic.cluster.predict" but not "oncotypedx" and "gene70" #15

Open PedroMilanezAlmeida opened 5 years ago

PedroMilanezAlmeida commented 5 years ago

Hey y'all,

It would be great if the help of "molecular.subtyping" and "intrinsic.cluster.predict" would indicate the need for a column called "probe" in "annot".

Right now it says only that at least one column named "EntrezGene.ID" (for ssp, scm, AIMS, and claudinLow models) or "Gene.Symbol" (for the intClust model) is needed, but a column called "probe" is also needed.

This is problematic because other functions such as "oncotypedx" and "gene70" require the rownames of "annot" to be the probe names, instead of a column called "probe" with the probe names.

It would be even better if this was unified (e.g., either "annot" always needs a "probe" column or it never does).

Cheers and thanks!

Puriney commented 4 years ago

Yes. The first column of the annot should be "probe", which should be as same as the col names of the data, otherwise error shows up:

Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent

ChristopherEeles commented 4 years ago

Hi @Puriney,

I will address this issue in the next update. It will likely take a few weeks though, as I am currently occupied with other projects.

Best, Christopher Eeles Software Developer Benjamin Haibe-Kains Lab Princess Margaret Cancer Centre

Puriney commented 4 years ago

No worry. The quick solution exists. We end-users can simply add one column named 'probe' and then the problem is solved. This issue, I guess, is to simply remind you to correct the description in the document.