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Multiple variables/interactions #211
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So, we haven't yet engineered any functionality for this explicitly as you have noticed. PRs welcome- the DESeq module is here: https://github.com/nf-core/modules/tree/master/modules/nf-core/deseq2/differential I haven't though hard about this but.... if you included the extra parts in the blocking column like |
Same issue here, any updated on this issue? Does the suggested solution work? |
Description of feature
Hello,
My experimental design is longitudinal (i.e. time series), and my main focus is finding DE genes in the interaction between treatment (yes/control) and time (T0....T6). My metadata header looks like this:
sample treatment time
The DESeq2 model would be something like:
Now, as far as I know, the contrast file only allows one variable and one reference level. Is there a way to use this pipeline for my case (two variables, two reference levels) with some contrasts magic? If not, can it be implemented?
Thanks
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