User: nobishvarghese

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Posts by nobishvarghese

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exonBaseMean calculation in DEXSeq
... Hello, I would like to know how 'exonBaseMean' in DEXSeq result is calculated.The documentation (http://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf , page 16,  under mcols(dxr1)$description) describes it as 'mean of the counts across samples in each feature/exon'. I ...
dexseq written 2.7 years ago by nobishvarghese0
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window counts in csaw
... All, I have a question on window counts generated by csaw.Could you share your thought on this? I  have MeDIP data on 3 conditions with 4 replicates each and matching input samples .So, i have 24 samples and it is paired end data. I have found that windowCounts function in csaw generate differing ...
counts csaw written 3.1 years ago by nobishvarghese0 • updated 3.1 years ago by Aaron Lun24k
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Detection of methylated regions from MeDIP data using csaw
... I tried to use csaw to compare samples from MeDIP data. My dataset has 4 conditions namely group1, group2, group3 and group4 with one ChIP and Input sample for each condition (unfortunately, we have only a single replicate per condition for now; because of this, I used glmFit function with a dispers ...
csaw medip-chip written 3.2 years ago by nobishvarghese0 • updated 3.2 years ago by Aaron Lun24k

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