Hi all,
I would like to determine whether RNA-seq RPKM values are expressed in a particular cell type or not. Let's say sort of a one sided t-test, which of course is not feasible because there are not so many replicates (N=2 or 3 per condition), and get p-values to determine the significance of expression.
I used tophat, cufflinks and cuffdiff to align data and calculate the RPKM values per sample, however, since I have 2 or 3 values per cell type and would like to determine the expression values based upon all samples, I don't know how to calculate these.
Cuffdiff gives an 95 % confidence interval around around the FPKM values per cell type, but these confidence intervals are not multiple testing corrected, and do not contain p-values.
Does anybody have an idea how I can test which genes are expressed in a particular cell type with the asssociated multiple testing corrected p-values based upon RNA-seq data?
Many thanks!
Kind regards,
IR
I would like to determine whether RNA-seq RPKM values are expressed in a particular cell type or not. Let's say sort of a one sided t-test, which of course is not feasible because there are not so many replicates (N=2 or 3 per condition), and get p-values to determine the significance of expression.
I used tophat, cufflinks and cuffdiff to align data and calculate the RPKM values per sample, however, since I have 2 or 3 values per cell type and would like to determine the expression values based upon all samples, I don't know how to calculate these.
Cuffdiff gives an 95 % confidence interval around around the FPKM values per cell type, but these confidence intervals are not multiple testing corrected, and do not contain p-values.
Does anybody have an idea how I can test which genes are expressed in a particular cell type with the asssociated multiple testing corrected p-values based upon RNA-seq data?
Many thanks!
Kind regards,
IR
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