I have done DEXSeq test for my C, L, S three conditions samples and got the html report like below:
I noticed that the log2 fold changes are caculated by the usage coefficient columns(c, l, s), but I am not clear that how those coefficients are caculated. I assume they are caculated based on statistic fomula described in the paper and vignette, but I couldn't understand it because of lacking related knowledge. So could anyone explain it for me in a understandable way?
In addition, I have a question about the "splicing" plot in the html report. I read the post:DEXSeq Usage and Expression Confusion In the post, Simon explained that the exon usage in splicing plot is by "averaging out effects of overall expression" I could understand the basic concept but I want to know that how the "average out" works and Is it related with the usage coefficients?
Actually, I want to do further filteration based on the exon usage value in the splicing plot, however these value are neither stored in the html report nor in the DEXSeqResults object, instead they are calculated during the plot process. So is there a way that could output the exon usage value?
Please give me any comments and answers, thanks a lot.