hello, I performed the differential analysis using the following pipeline, trimmomatic → kallisto quant → deseq . I get the volcano plot on the screen below using the volcano plot tool with Significance threshold = 0.05 .
there is a lot of genes at the top, what’s wrong with it ? if it’s normal what’s the interpretation of it ?
Hi @azzahrae,
could you try to sort the DESEQ result file according to the p-values and share a screenshot of it? I think that the plot is fine, just those genes at the top are those whose p-value is extremely low.
Regards
hi @gallardoalba, the attached field is the result of deseq without sort, there is some problem in the galaxy server I can’t do the sorting task.
deseq2 result
Hi @azzahrae,
it seems that some genes show such a low p-value that is considered as 0 (because the smallest floating-point value in R is 2.225074e-308, so anything smaller is rounded to 0), and the -log of a number tending to 0 is infinite.
Regards
thank you, what we can say about these genes as an interpretation?
According to the DESeq2 results, you could hypothesize that those genes are the most relevant from a biological point of view (the ones whose differential expression is more significant from a statistical point of view). But anyway, I suggest you consider in the downstream steps all those genes whose Adjusted p-value is lower than 0.05.
Regards
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