Question: How to combine p-values of differentially expressed genes from different timepoints
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gravatar for Ambika
10 weeks ago by
Ambika30
United States
Ambika30 wrote:

Hello everyone,

I have the list of differently expressed genes from DESeq2 for three different timepoints. I have few genes that are differentially expressed in all three timepoints for which I want to combine the p-values to get one. I was thinking of taking an average p-value, but looks like that is a wrong way. Also, is it ok to average the Log2FoldChange values of these genes too?
Can you suggest any r packages or methods to combine the p-values and Log2FoldChange values.

The three timepoints are from the same biological sample and same treatment condition.

Thank you, Ambika

rna-seq p-value • 207 views
ADD COMMENTlink modified 24 days ago by Biostar ♦♦ 20 • written 10 weeks ago by Ambika30
1

What question are you trying to answer by doing this? There might be a more direct way to address it.

ADD REPLYlink written 10 weeks ago by rpolicastro2.3k

I am doing gene enrichment analysis of differentially expressed genes using TopGO for which I need p-value of the listed genes. In my case I have 3 different p-values from three timepoints. I am looking for a way to combine these p-values to one so that I can proceed further.

ADD REPLYlink written 10 weeks ago by Ambika30

Can't you just take the maximum p-value (max_p) from these few genes and report it as p <= max_p. You can do the same with the foldchange.

ADD REPLYlink written 10 weeks ago by a.zielezinski9.3k

The program I am going to use does the hierarchical distribution based on p-value so I don't think I can do that. I need an exact p-value.

ADD REPLYlink written 10 weeks ago by Ambika30

Hi, Please, wich program you are using for hierarchical distribution? When I performed any kind of expression analysis (RNAseq or even microarray) with multiple factor (time, dose, tissue, etc) the programs usually have options to carry on with all the conditions OR you simply work with each dataset separately. I never heard anything about "combine p-values" in order to execute any downstream analysis. IMPORTANT: It is recommended to consider the adjusted p-value for the significance of genes.

ADD REPLYlink modified 23 days ago • written 23 days ago by Arsenal20
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