Question: Transforming RNA-seq data- (tpms) - what is the best practice for dealing with zeros for the purpose of deconvolution?
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gravatar for nancy
4 months ago by
nancy70
nancy70 wrote:

Using Cibersort to deconvolve bulk RNA-seq data to specific cell-types based on expression values from bulk RNA-seq. I have a series of samples, and their individual TPMs as computed by Stringtie. Each column is a sample, each row is a gene. Since cibersort only accepts non-zero values, I am trying to understand the best way to transform those tpms which = 0.

Are any of the below more preferred/accurate?

  1. Treat all samples and all rows the same- Add a small (0.0001) value to all the rows for all samples
  2. Treat all samples the same for those rows which = 0 - Add a small (0.0001) value to only those rows with 0
  3. Treat each sample differently - Find the smallest non-zero value for each sample, and add that value toall the rows for that sample.

Thanks

ADD COMMENTlink written 4 months ago by nancy70

What do the authors of Cibersort do in their paper?

ADD REPLYlink written 4 months ago by kristoffer.vittingseerup1.7k
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