Differentail gene expression results

Question

[ahmad.sajad4541]

can anyone suggest me about the results of differential gene expression analysis using DESeq2. i have 10 samples, of which 6 are disease and 4 are healthy, i have find the raw counts and now i have run the following code on my data . Note" i have't collapse/merge the samples"

the output results of this is

[ATpoint]

What is your question?

See https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html which covers most relevant aspects for beginners.

General notes:

• your prefilter (keep) is basically not doing anything relevant other than removing genes that are only zero, see the vignette on prefilters
• do some basic QC, for example PCA; see vignette
• plot results, e.g. MA-plots, see vignette

[swbarnes2]

Cross-posted: https://support.bioconductor.org/p/9158194/