Hello!

I want to use DESeq2 to identify genes that are differentially expressed across 10 genotypes ranked by restoration value (resval). However, I want the numbers to be seen as numerical, not categorical, as the rank order matters. Currently, my code is set up like this.

dds<-DESeqDataSetFromMatrix(countData=countstrim,colData=conditions,design = ~ resval)

when I type

resultsNames(dds)

the output is [1] "Intercept" "resval_2_vs_1" "resval_3_vs_1" "resval_4_vs_1" "resval_5_vs_1" "resval_6_vs_1" "resval_7_vs_1" "resval_8_vs_1" [9] "resval_9_vs_1" "resval_10_vs_1"

Which indicates to me that DESeq is seeing these numbers as categories. I want to see what genes are being differentially expressed for each restoration value rank, not compare the categories in this predetermined manner.

Please let me know if I'm thinking about this in the wrong way or how to proceed with this?

Thank you!

How did you import the data? Did you accidently leave in stringAsFactors=True?

But I'm not entirely sure that you don't want that to be true. You might want to keep them as factors, and do an LRT comparison instead of pairwise. If you keep them as numerical, it will try to fit a linear curve, as if the numbers were days, or doses, and I'm not sure that's what you want.