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user 17761
2
votes
1
answer
71
views
DE analysis tool and method for non-coding features
Among the three DE test methods in edgeR such as exactTest(), glmFit() and glmLRT(), glmQLFit() and glmQLFTest(), which is/are the one(s) most suitable for running DE tests on miRNA, snRNA, snoRNA, pseuogenes … Should I be using any other DE analysis tool instead of edgeR for some specific non-coding feature, like there's lncDIFF for lncRNA? …
1
vote
1
answer
45
views
Statistical methods suitable for DE analysis of non coding RNAs
I am currently working on DE analysis of coding as well as non-coding features of A. thaliana using the edgeR package. … Also, among the various DE test methods in edgeR such as exactTest(), glmFit() and glmLRT(), glmQLFit() and glmQLFTest(), which is/are the one(s) most suitable for running DE tests on such non-coding features …
1
vote
1
answer
78
views
Filtering criteria for non-coding features with very low counts
Now, for the DE analysis of coding features, an inbuilt filtering method to remove the extremely low counts is available in edgeR, called filterByExpr(). …