what is the function of prior.count in lcpm ?
In this command line while using edgeR, lcpm<-cpm(y,prior.count=5, log=T)
what is the applicability of prior.count there ?
I found "prior.count as average count to be added to each observation to avoid taking log of zero. Used only if log=TRUE."
Is there any range to be used ? How to know which threshold is right ?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
edgeR customized normalization for differential analysis
written by Wu-Sheng Zhang •
-
Help in Log2 transform CPM count
written by G.S •
-
filtering lowly expressed reads
written by Shaimaa Gamal •
-
[R] Differential Co-Expression ?
written by ali •
-
[R] Extract Normalized Counts from DGEList (edgeR) ?
written by ali •
-
CPM function in EDGER
written by francesca3 •
-
Which counts to use for RNA-seq heatmap and PCA?
written by Lucy •
-
Problem with low count removal in edgeR ?
written by Björn •
-
Should I remove samples after normalization of miRNA seq read counts ?
written by Björn •
-
edgeR normalization and partial correlation matrix calculation
written by moxu
Log zero will
-Inf. Adding aprior.countwill make the logged value be countable. Theprior.countshould be small, like the default 0.25 or the min ofyexcept 0 to weaken the effects ony.