Question: How to create a covariate file for MutSigCV using gene expression values from other resources.
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gravatar for luca.zammataro
3.1 years ago by
USA, New Haven, Yale University
luca.zammataro0 wrote:

Hi, I wish create a covariate file as input for MutSigCV, using expression values from a specific gene expression data set. Someone knows how to do this? Moreover, analyzing the covariate file provided by the author of the software, in the Example Data, i noted that the global expression values are represented by numbers that I cannot understand.

i.e.:

gene expr reptime hic

A1BG 1621097 406 -25

A1CF 113129 613 19*

What do those numbers mean? Are they microarray expr values? Or are they values from some RNAseq conversions (FPKM or RPKM) ? Someone knows what exactly means "1621097" for the A1BG gene, and "113129" for the A1CF? Digging in the MutSigCV documentation I haven't found explanations about that. Thank you, Luca.

ADD COMMENTlink written 3.1 years ago by luca.zammataro0

Having the same question here, did you find out where this value comes from?

ADD REPLYlink written 7 months ago by sm.hashemin90
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