Question: Deseq2 design for repeated measure
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gravatar for mila.grinblat
5 months ago by
mila.grinblat0 wrote:

Hi I saw many posts about this topic but they never actually answered the specific question I have so I am sorry if this was asked before I am looking at miRNA expression in corals, in different months in males and females. I do sample the same individual every month but it gets a bit tricky as the different months are not necessarily a time series but more of a specific biological point (reproductive cycle) and not a treatment. I need to use repeated measure ( I think so) as I am sampling the same biological individual I am trying to find the deferentially expressed miRNA in males vs. females in general and find out which different miRNA expressed in each month (and will be assosiated to the stage of the oogenesis or spermatogenesis . the samples I have are not balanced as well: Sample (just the uniqe name in the seq) Month (timepoint Sex (M or F) name (the actual name of the coral sampled more than ones)

Sample Month Sex name F01 July Female Ff46 F02 July Female Ff27 F03 July Male Ff62 F04 July Male Ffff13 F05 Aug Female Ff46 F06 Aug Male Ffff13 F07 May Female Ff27 F08 May Female Ff46 F09 May Male Ff54 F10 May Male Ff62 F11 May Male Ffff13 F12 May Male Ffff15

I know that in a repeated measure anova, my design will look something like that Gene expression count~sex+Month +Error(Sample) But I am not sure how it works in deseq2 or any other DE analyses (my background is in ecology) how do I add the "error" to be taken under account?

Thanks and let me know if more information is needed

deseq2 • 100 views
ADD COMMENTlink modified 5 months ago by Michael Love25k • written 5 months ago by mila.grinblat0

and the data as a table

ADD REPLYlink written 5 months ago by mila.grinblat0
Answer: Deseq2 design for repeated measure
0
gravatar for Michael Love
5 months ago by
Michael Love25k
United States
Michael Love25k wrote:

If you have complex correlations among samples, you may want to try duplicateCorrelation in the limma-voom pipeline instead

ADD COMMENTlink modified 5 months ago • written 5 months ago by Michael Love25k
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