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How to filter up and down regulated genes in a list of DE genes from DEseq?

I got some gene expression data sorted from differential expression analysis (used only significant genes <0.05 padj). I need to write the data in to a csv file with the following column names, Condition, Genes (up and down in each condition), counts (sum of genes either up or down regulated).

I can provide further information as needed.

upanddownregulated genes
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updated by lmlukoseviciute • lmlukoseviciute • written by arulin • arulin

Please be more clear about the data structures that you have. But if you are working with locus tags instead of gene names you can get filtered locus tags by

loc_tags = rownames(results)

assuming you have your results from deseq2 in object results. And then by going through your data frames by these indexes you can extract information you want.

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written by lmlukoseviciute • lmlukoseviciute

1 answer

What is the original data file format? How the data is being arrange? Can you load it into excel and use filter function to seperate it?

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written by qmarulfiz qmarulfiz

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