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Question: deseq2 output interpretation problrm
1
gravatar for shafnaasmy.v.s
18 months ago by
shafnaasmy.v.s • 10
shafnaasmy.v.s • 10 wrote:

hi

i did my DeSeq2 from the results from htseq-count

my input was 3 control and 6 test

htseq-count result uc001aak.4 0 uc001aak.4 0 uc001aak.4 0 uc001aak.4 0 uc001aak.4 0 uc001aak.4 0 uc001aak.4 0 uc001aak.4 0 uc001aak.4 0 uc001aak.4 2 uc001aak.4 0

the result from deseq2 is like this

uc060kef.1 180.5926675 -1.306161383 0.152473325 -8.566491098 1.07E-17 1.38E-13 uc060tgd.1 992.195252 -1.447544241 0.178611927 -8.10440974 5.30E-16 3.44E-12 uc058mvb.1 478.1811761 1.025237773 0.173633756 5.904599395 3.54E-09 1.53E-05 uc003pil.2 427.5855981 0.770298658 0.140736599 5.473335739 4.42E-08 0.000114544 uc061zxt.1 82.21639908 -0.986557914 0.179465594 -5.49719807 3.86E-08 0.000114544 uc062zbc.1 47.11435901 -0.8895186 0.178256468 -4.990105618 6.03E-07 0.001304284 uc001ogf.4 141.6566029 -0.834506687 0.170421261 -4.896728753 9.74E-07 0.001598306 uc061qlz.1 183.5004481 -0.821882633 0.167922646 -4.894412118 9.86E-07 0.001598306 uc061zcf.1 62.93212095 -0.808181912 0.183024186 -4.415711005 1.01E-05 0.014506656

how do i interpret...i am not really clear with it ....

how do i find the downregulated and upregulated genes from this result

plz help..

shafna
rna-seq deseq2 • 1.0k views
ADD COMMENT • link •
modified 18 months ago by Devon Ryan • 1.9k • written 18 months ago by shafnaasmy.v.s • 10
1
gravatar for Devon Ryan
18 months ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:

The columns are described at the bottom of DESeq2's page in Galaxy:

Column  Description
1   Gene Identifiers
2   mean normalised counts, averaged over all samples from both conditions
3   the logarithm (to basis 2) of the fold change (See the note in inputs section)
4   standard error estimate for the log2 fold change estimate
5   Wald statistic
6   p value for the statistical significance of this change
7   p value adjusted for multiple testing with the Benjamini-Hochberg procedure which controls false discovery rate (FDR)

Differentially expressed genes are those with an adjusted p-value (column 7) below the threshold you desire (typically 0.05 or 0.1). Whether they're then up or down-regulated is dictated by the sign on the log2 fold-change (column 3).
ADD COMMENT • link written 18 months ago by Devon Ryan • 1.9k
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