Hello :)
I have a RNA-seq dataset and a ChIP-Seq dataset and I have ran a differential binding analysis and differential expression analysis, both using DESEQ2.
For the RNA-seq I have just followed a standard and the resulting tsv has the following columns:
......,log2Foldchange,lfcSE,pvalue,padj
For the ChIP-Seq I have used diffbind to perform the deseq analysis, and extracted the deseq2 object using DBA.report and and now it has the following columns:
...., Conc, Conc_x,Conc_y, Fold, p-valule, FDR
When I plot both the fold changes (log2FoldChange vs Fold) in a scatterplot it does not appear that these are calculated equally. The RNA DESEQ fold changes appear to be evenly disributed over a range (-4 to -4), with alot of genes showing no major changes. The diffbind DESEQ2 analysis however yield a strange scatterplot pattern where there are no significant samples with a fold change between 1 and -1.
My question is if these DESEQ2 fold changes are calculated equally? If not how should I go about applying the same log2foldchange formula to both datasets?
I am very happy to clarify should something be unclear :)
Best,
Marc
