Number of upregulated and downregulated genes from counts matrix

Question

[taniamahmood38]

Hi, I am doing differential gene expression analysis on two datasets using trinity toolkit. Now i have TMM expression counts matrix, MA plot, Volcano plot, heatmap etc. I want to know the exact number of upregulated and downregulated genes in my dataset. Is there any tool which can help to count it ? My dataset is large, so counting it manually will be a cumbersome process. Waiting for quick response....

Thanks in advance!

[Pratik]

Could you share a sample of your counts matrix?

I'm not familiar with trinity (I'm not sure if there are built in functions within trinity to do what I'm suggesting below)

If you just want to know which genes have positive expression values and which genes have negative expression values or if you have some sort of threshold which indicates downregulated and upregulated, using your count matrix, you could probably write a bash or R script to extract the downregulated to genes to one list, and upregulated genes to another list, and then use (if you transfer the resulting file to bash terminal) like cat upregulatedgenes.txt | sort | uniq | wc -l and then you could repeat it for downregulated cat downregulatedgenes.txt | sort | uniq | wc -l this would give you the number of genes in that text file.

That's how I would do it on the fly. I'm sure there is probably a better way.

[taniamahmood38]

Yes, trinity is a command line tool. It makes use of R packages for differential gene expression analysis (EdgeR, DSeq2, limma etc.) . Anyways, I am really grateful to you for the help. Many thanks.