User: teshome.dagnem

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Posts by teshome.dagnem

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Comment: C: edgeR cpm filter
... The user manual is clear and tried to follow the reasoning, for example section 4.2.4. I was a bit confused with section 2.6 and that is why i say arbitrary. "As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples for any of the conditions" and it provides how t ...
written 4 weeks ago by teshome.dagnem0
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Comment: C: edgeR cpm filter
... Now, we agree that the filter shouldn't be per sample. Then, is it an arbitrary choice? If yes, how do we decide the optimal threshold for the rowSum? ...
written 4 weeks ago by teshome.dagnem0
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Comment: C: edgeR cpm filter
... Do you think >=5 is a reasonable threshold to all 167 libraries? ...
written 4 weeks ago by teshome.dagnem0
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Comment: C: edgeR cpm filter
... When i say "this doesn't work", the rowSums >=5 is filtering across all columns (167 samples) rather than per sample for the 6 replications. I double checked the dataset after the filter and i confirm the results. We can also extend our discussion using the following reproducible example: data ...
written 4 weeks ago by teshome.dagnem0
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Comment: C: edgeR cpm filter
... > summary(RG.1$samples$lib.size)     Min.  1st Qu.   Median     Mean  3rd Qu.     Max.  11330000 21890000 23870000 23900000 26330000 37230000 ...
written 4 weeks ago by teshome.dagnem0
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edgeR cpm filter
... Hi, We have a three factor RNA-Seq experiment result from 167 samples (6 replications per sample). Factor 1 = salinity, level = 2 (fresh water, salt water) SALINITY <- c(rep(rep(c("FW","SW"), each=6), 7), rep(c("FW","SW"), c(5,6)), rep(rep(c("FW","SW"), each=6), time=6)) Factor 2 = photoperi ...
edger independent filtering multiple factor design cpm written 4 weeks ago by teshome.dagnem0 • updated 4 weeks ago by Gordon Smyth32k

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