User: Darklings

gravatar for Darklings
Darklings0
Reputation:
0
Status:
New User
Location:
Last seen:
1 week, 4 days ago
Joined:
5 months, 3 weeks ago
Email:
p*******@gmail.com

Posts by Darklings

<prev • 4 results • page 1 of 1 • next >
0
votes
2
answers
140
views
2
answers
Comment: C: Get the countsFromAbundance as limma input
... I just drew the logCPM density plot, then I saw some weird lines in both raw & filtered plots (I have highlighted them with blue boxes):  https://drive.google.com/open?id=1qIvW-fiO3MC1QA_0-5putL307Brx7N6h I filtered the data using the filterByExpr() function. Do these lines mean some samples ha ...
written 15 days ago by Darklings0
0
votes
2
answers
140
views
2
answers
Comment: C: Get the countsFromAbundance as limma input
... Hi Smyth, thanks for your suggestion. Actually I tried both limma-trend and limma-voom, they didn't cost too much time. I found that if using limma-trend, the p-values in toptable are much higher and logFC are much smaller than those in limma-voom's. The following is my code: # limma-voom: v0 < ...
written 17 days ago by Darklings0
2
votes
2
answers
140
views
2
answers
Get the countsFromAbundance as limma input
... I am analyzing the TCGA data and doing the differential expression analysis for about 6,000 samples and 20,000 coding genes. I was suggested to use DESeq2 for DE analysis, but the DESeq() takes an extremely long time with 6,000 samples, therefore I would like to use the limma-voom instead. In the t ...
limma deseq2 differential expression tximport written 21 days ago by Darklings0 • updated 20 days ago by Gordon Smyth35k
2
votes
1
answer
184
views
1
answer
Error in ebayes in limma when analyzing GTEx data
... Hi there, I am building a linear model to analyze the expression profiles of cvd and non-cvd subjects. There are 227 samples here.  When fitting the model: design = model.matrix(~ race + age + bmi + gender + batch + cvd + subject) fit = lmFit(voomOutput, design) fit = eBayes(fit) tt  = topTable( ...
limma voom gtex written 5 months ago by Darklings0

Latest awards to Darklings

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 2.2.0
Traffic: 331 users visited in the last hour