Question: Identifying DEG from time course data without condition
0
gravatar for ChIP
3.8 years ago by
ChIP570
Netherlands
ChIP570 wrote:

Hi,

I have a a time course data for 7 time points with 3 replicates each and I would like to point out the clusters of genes that are differentially expressed in at least one group Vs others.

Similar problems with control and treatment problems can be solved with DESeq2 but I don't have 2 condition model.

Kindly, let me share your knowledge.

Thank you.

rna-seq edger deseq • 1.0k views
ADD COMMENTlink modified 3.8 years ago by Benn8.0k • written 3.8 years ago by ChIP570
2

Section 3.4 in DESeq2 vignette tells you how to analyze time series data.

ADD REPLYlink written 3.8 years ago by genomax89k
1
gravatar for Benn
3.8 years ago by
Benn8.0k
Netherlands
Benn8.0k wrote:

If you use edgeR, you can follow the ANOVA-like test in the manual.

ADD COMMENTlink written 3.8 years ago by Benn8.0k

Hi,

I am also trying to compare multiple samples by EdgeR with ANOVA-like approach.

I would like to get all the FC and P-value, FDR for all comparison.

After looking on forums and reading the manuals, I am still not able to obtain the information which comparison is significant, is there a way to do this? By following the manual I am only getting FC values for the different comparisons and a single P-value, FDR. Am I missing something?

Thanks you.

ADD REPLYlink written 11 months ago by hlsz.laszlo20
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