Question: could the result of DEseq2 by LRT be used in SPIA directly?
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gravatar for qq809825706
10 weeks ago by
qq8098257060 wrote:

the LRT in DEseq2 make the similar format results to wald test, but log2FoldChange has another mean which I can't understand. so I wonder if the result of DEseq2 by LRT could be used in SPIA or GSEA directly. If not, how to apply it with SPIA or GSEA? could anyone help me? thank you.

deseq2 • 99 views
ADD COMMENTlink modified 10 weeks ago by Michael Love25k • written 10 weeks ago by qq8098257060
Answer: could the result of DEseq2 by LRT be used in SPIA directly?
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gravatar for Michael Love
10 weeks ago by
Michael Love25k
United States
Michael Love25k wrote:

I am not familiar with SPIA.

You can use the adjusted p-values from a Wald or LRT. With the LRT, just make sure you read the information in ?results about how multiple coefficients can be tested at once depending on the full and reduced designs and the number of levels of the factors involved.

ADD COMMENTlink written 10 weeks ago by Michael Love25k

thank you for your reply. I'm doing a Time course analyses (2 treatment and 5 time point) with LRT refer to Hypothesis testing: Likelihood ratio test (LRT). but it mention:

even though there are fold changes present they are not directly associated with the actual hypothesis test

and

We are unable to set a fold change criteria here since the statistic is not generated from any one pairwise comparison.

so. I was confused whether I can use the fold change to the GSEA or SPIA analysis after clustered by degPatterns directly like in Wald.

ADD REPLYlink written 9 weeks ago by qq8098257060

If you want to focus on a fold change and a p-value associated with one fold change then just use the Wald test p-values.

ADD REPLYlink written 9 weeks ago by Michael Love25k
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