Question

mirna-mrna interation mircomb (from DEGs and DEMs lists)

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andreia ▴ 10

@andreia-23745

Last seen 2.6 years ago

Portugal

Hi there, i am stuck here in the analysis of mirna-mrna interactions because i migrate from deseq2 to mircomb and according to the paper of package you can add any format, but you need to have the specific columns if you want to do from DEGs/DEMs lists. They are the FC, logratio, mean expression, pvalue and adjusted p value. So i am very confusing with logratio and mean expression with baseMean values from DESeq2... Can you help me with this?

Thanks in advance.

deseq2 mircomb degs dems • 943 views

ADD COMMENT • link updated 4.4 years ago by Michael Love 42k • written 4.4 years ago by andreia ▴ 10

score 0 · Answer 1 · 2020-06-29

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Michael Love 42k

@mikelove

Last seen 15 hours ago

United States

Please read over the DESeq2 documentation. These values are all clearly described as part of the output. See the rnaseqGene workflow in particular (for beginners).

ADD COMMENT • link 4.4 years ago Michael Love 42k

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Thanks Michael for the fast reply :)

Its hard sometimes do get the answers that you need when you have a strictly deadline and the documentation, papers and others have different names to the same thing!

With help of my bioestatistician i have got confidence what i am doing before showing the client...

So, from DESeq2 if you need to use the lists of DEGs and DEMs on miRComb you need to:

log2foldchange = logratio
2^log2foldchange = FC
pvalue=pval
padj=adj.pval
log2(baseMean)=meanExp

After that you can apply this code to add the corObj:

mydata.obj@diffexp.mRNA<-degs
mydata.obj@diffexp.miRNA<-dems
mydata.obj<-addSig(mydata.obj,"mRNA",adj.pval=0.05)
mydata.obj<-addSig(mydata.obj,"miRNA",adj.pval=0.05)
mydata.obj@info$mRNA.diffexp.method<-c("DESeq", "DvsC")
mydata.obj@info$miRNA.diffexp.method<-c("DESeq", "DvsC")

ADD REPLY • link 4.4 years ago andreia ▴ 10