Hi, I'm trying to analyse some RNA-Seq data via volcano plot. I've managed to make the plots well enough and can identify genes of interest based on the cutoffs, however I'm noticing a certain amount of "noise" in the form of genes which have high fold-changes but low p-values (see attached). I've checked the counts for these genes and they seem to be transcripts with very low counts (ie 2 in one sample and 16 in another).
Other volcano plots i've seen seem to have a nicer shape, with all low p-value genes also having minimal fold-changes.
To me this suggests that either the magnitude of the fold-changes in their DEGs far exceeds the ones I have, or else people are filtering the data to remove low-abundance transcripts before making the volcano plot?
Any advice?
I would not be concerned that much with low FC/low p-value. This would happen.
What I see as a potential problem are the crazy low p-values (or high if you look at -log10). This does not look normal and it distorts the typical volcano look of the volcano plot. Essentially what this tells me is that you have genes that are completely missing in one condition and present at high levels and low variability in another. Not impossible, for example if you compare very different cell types.
So if this is the case perhaps your plot is OK. Little more background could help us answer your question.
And here is an example of plots similar to yours (Figure 2):
https://www.researchgate.net/publication/325696186_Brain_Cell_Type_Specific_Gene_Expression_and_Co-expression_Network_Architectures/figures?lo=1
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