Deseq2 - how to save zero counts on normalization step

Question

[Sandhiya]

Hi all,

I have raw read counts [of rna-seq]. I need to normalize this data and have done it using DESeq2. But, I found that DESeq2 eliminates the read counts of genes when it's equal to 0. I don't want to lose this data as it might affect my result.

Is there any way to do the normalization without eliminating zero read counts?

Thanks in advance.

[swbarnes2]

The author suggest removing empty genes are you sure you know better than he? I think empty genes are not removed by default, so can't you just not remove them?

Genes with read count 0 will be ignored when normalizing. They have to be.

[Sandhiya]

@swbarnes2 I don't compete OR get into argument with what authors say.. I'm writing my requirement and how I can find a solution for it.

Answer 1

[jared.andrews07]

DESeq2 does not remove any genes by default (0 counts or not). Your results will contain all genes, though those that don't pass independent filtering due to low expression will have adjusted p-values set to NA.

Similarly, 0's are not removed from the normalized counts, e.g. min(counts(dds, normalized = TRUE)) will still be 0.

[Sandhiya]

Thank you @jared.andrews..

I have solved this ..