Hi all,

I'm trying to figure out the options of the new DESeq2 function "unmix". In my case, I have normalized gene counts for : primary breast tumor, ovarian metastasis, and normal ovary of the same individual. The "unmix" function is:

unmix(x, pure, alpha, shift, loss = 1, quiet = FALSE)

apparently "x" in this case would be the ovary metastasis. my question is what would be the pure sample in this case? the primary tumor or the normal ovary? and the other question is what kind of output I'll get from this function? is it corrected gene counts?

Thank you,

Ahmed

The "pure" argument is asking for a matrix of the pure components. unmix() will estimate, for every column in "x", a combination of columns of "pure" that best explains it. If you take a look at the help page there is some more information:

?unmix