The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

User: teshome.dagnem

Reputation:
0
Status:
New User
Last seen:
1 year, 4 months ago
Joined:
1 year, 4 months ago
Email:
t*************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by teshome.dagnem

<prev • 6 results • page 1 of 1 • next >
0
votes
1
answer
602
views
1
answers
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 16 months ago by teshome.dagnem0
0
votes
1
answer
602
views
1
answers
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 16 months ago by teshome.dagnem0
0
votes
1
answer
602
views
1
answers
Comment: C: edgeR cpm filter
... Do you think >=5 is a reasonable threshold to all 167 libraries? ...
written 16 months ago by teshome.dagnem0
0
votes
1
answer
602
views
1
answers
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 16 months ago by teshome.dagnem0
0
votes
1
answer
602
views
1
answers
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 16 months ago by teshome.dagnem0
4
votes
1
answer
602
views
1
answer
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 16 months ago by teshome.dagnem0 • updated 16 months ago by Gordon Smyth36k

Latest awards to teshome.dagnem

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 318 users visited in the last hour