Hello all,

I would like to calculate TMM normalization for identifying DE genes. I know that edgeR does all the normalization when you run the code but I would like to calculate TMM for one or two genes to manually to better understand the statistic behind it. I found this formula to do so ( below) but I am not sure what the component, factor means?

(raw.counts)*10^7/(librarysize*factors)

librarysize=total number of mapped reads.

I would really appreciate any suggestions and help.

Thanks !

I would like to calculate TMM normalization for identifying DE genes. I know that edgeR does all the normalization when you run the code but I would like to calculate TMM for one or two genes to manually to better understand the statistic behind it. I found this formula to do so ( below) but I am not sure what the component, factor means?

(raw.counts)*10^7/(librarysize*factors)

librarysize=total number of mapped reads.

I would really appreciate any suggestions and help.

Thanks !

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