[BioC] TMM Normalization without replicate
Jieon Lee [guest]
guest at bioconductor.org
Wed Feb 13 07:23:59 CET 2013
Hi, I am a graduate student at POSTECH and I ran into some troubles while running edgeR program.
Currently I have six Chip-Seq samples, all of different condition. There are no biological replicate and no control sample.
So when I try to run edgeR, it does not run for there is no biological replicate used for statistical testing.
I wonder if there is a way to export TMM normalized count from edgeR package without compliting the program.
I know the program should run up till calcNormFactor and give normfactor but without biological replicate, it cannot calculate dispersion and the whole program fails to run.
Is there a way to export just the TMM normalized data without doing statistical testing?
If so, what are the codes that allow such methods?
I tried cpm function but cpm may use raw or normalized data not gives a normalized data from raw data.
Thanks in advance,
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