RNAseq matrix containing zero values

Question

[rupali]

this file contains rnaseq data matrix for the DEGs my question is that do we have to remove the sample containing 0 value before starting the analysis.

[benformatics]

Removing un-expressed genes is pretty standard

[Nicolas Rosewick]

Please do not use excel for bioinformatics purpose : https://nsaunders.wordpress.com/2012/10/22/gene-name-errors-and-excel-lessons-not-learned/

Answer 1

[Shred]

Personally I won't not continue with the analysis using Excel. As in the wet lab, you must follow a procedure, which needs to be tracked, reproducible and readable: with Excel this is not possible, even if you're so crazy to script all the procedures using VBA. Here's the most comprehensive, yet simple for beginners, walkthrough analysis of RNAseq data analysis using R and the library DESeq2 https://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

Just to answer the question, I'll add a column with the function =COUNTIF($START:$END, 0), where $START is the first sample column (ex. B1) and $END is the last sample column (ex. G1), which returns the amount of columns with 0s. Then I'll filter the matrix using this column.