Question: Multiple DEGs matrices
1
gravatar for asamie333
4 months ago by
asamie3330
asamie3330 wrote:

Bioinformatics novice here. I have multiple excel files each with a DEGs table, for cell type X (from Sc Rnaseq). How to best merge the matrices? By gene column? Across conditions? Somehow normalize and standardize first? Since the matrices some from different experiments? Batch effect? Apologies for silly questions, and thank you for kind answers. Sam

rna-seq • 114 views
ADD COMMENTlink written 4 months ago by asamie3330
1

That strongly depends what these data are and what your analysis goals is. First of all, why are there multiple tables? What do they contain, so which comparisons did you make and what is the question you want to answer? With DEG you mean results of differential expression? Please add details.

ADD REPLYlink written 4 months ago by ATpoint36k

Apologies for late reply. So to be more clear, I have differentially expressed genes matrices (LFC, p value and fdr) following Deseq2 for a given experiment eg. mutant1/wt. And multiple such independent experiments eg. mutant2/wt2, mutant3/wt3 etc. Though the number of genes detected are more or less the same, the gene ID are not. So when I simply combine the tables by gene ID column, ofcourse many of the rows give NA (because that particular gene was only detected in, say, one of three experiments). Should I (1) remove those NA rows? (2) make them into zero? I guess what I want is; column 1 = gene ID, column 2 = logfc-experiment 1, logfc-experiment two? Am I on the right track?

ADD REPLYlink written 5 weeks ago by asamie3330
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