gravatar for Aynur

2 hours ago by

Hello,
I am new to bioinformatics, and I am trying to do DEG analysis using DESeq2.
I followed the DESeq2 vignette, and I did this

res <- results(dds, lfcThreshold = log2(2), alpha = 0.05)

summary(res)

out of 17813 with nonzero total read count.                                                                                                                      
                        adjusted p-value < 0.05
LFC > 1.00 (up)    : 78, 0.44%
LFC < -1.00 (down) : 106, 0.6%
outliers [1]       : 0, 0%
low counts [2]     : 2073, 12%
(mean count < 7)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

So, my question is, how do I get my up-regulated and down-regulated genes from this output? I am setting my log2fc=1 for the cutoff threshold.
I also read this thread, but I still could not find the answer I am looking for.
Thank you very much.

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modified 2 hours ago

by

genomax90k

written
2 hours ago
by

Aynur20



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