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I have a set data set from genes derived from two populations, then I want to assess if the two populations have these genes differentially expressed. That's why I want to obtain the adjusted p-value.

I know little about coding, but I have tried without any success. I have tried Python and R.

The data that I have have this structure:

,CONTROL1,CONTROL2,CONTROL3,PROBLEM1,PROBLEM2,PROBLEM3
gene1,31.7,6.31,0.632,0.021,0.159,0.026,
gene2,31.7,6.31,0.632,0.021,0.159,0.026,
gene3,31.7,6.31,0.632,0.021,0.159,0.026,
...
gene_n,31.7,6.31,0.632,0.021,0.159,0.026,

I have tried all I found in Internet, but nothing succeeds.

I want to obtain a list similar to this:

gene_name, adjusted_p-value
gene1, 0.001
gene2, 0.3
gene3, 0.9
...
gene_n, 0.004

if someone could give me any hint where to check or how to do it I would be very grateful. Thanks!!

Sebastian
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    Stack Overflow is for specific programming questions, but you can't add an adjusted p-value to your dataset if you haven't calculated it yet. You first need to calculate the p-values, which means you need to decide which statistical test to use. This will depend on the study design and the variables of interest. – Andrea M Apr 12 '22 at 10:45
  • how do you go from your input table to the output? you need some formulas and algorithm to do the calculations. when you have them you can think on a way of implementing it. –  Apr 12 '22 at 11:23

1 Answers1

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Short answer is if you're using differential expression data it's probably worth using deseq2.

https://bioconductor.org/packages/release/bioc/html/DESeq2.html

The tutorial is pretty good: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

It walks you through how to go from a count matrix data which is basically what you have to a set of adjusted p-values.

For future things like this you might have a better time going to https://bioinformatics.stackexchange.com/ than here.

Sethzard
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