The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor
User: zhouqz
zhouqz • 0
- Reputation:
- 0
- Status:
- New User
- Last seen:
- 5 months ago
- Joined:
- 5 months, 1 week ago
- Email:
- h*********@126.com
Profile information, website and location are not shown for new users.
This helps us discourage the inappropriate use of our site.
Posts by zhouqz
<prev
• 5 results •
page 1 of 1 •
next >
0
votes
1
answer
207
views
1
answers
... I just want to know why base on the definition of logFC. You and Gordon are right. the actual logFC is base on the coefficient. Thanks again.
...
written 5 months ago by
zhouqz • 0
0
votes
1
answer
207
views
1
answers
... I manually remove the batch effect with weights base on the function of removeBatchEffect. However, the result still does not match to the autal logFC of topTable.
rv <- voom(x, design, plot=FALSE)
design.BatchEffect=model.matrix(~0+group)
batch <- as.factor(x$samples$lane)
contrasts(batch) ...
written 5 months ago by
zhouqz • 0
0
votes
1
answer
207
views
1
answers
... Dear Gordon,
Thank you very much for your reply. I have removed the batch effect, but the subtraction of means still does not matches the actual logFC. I have displayed the test code. Is it ok?
...
written 5 months ago by
zhouqz • 0
0
votes
1
answer
207
views
1
answers
... Dear Aaron,
Thank you very much for your answer. I saw the code of lm.wfit. I can get the coefficient base on the v$E and v$weight. But I do not know how to get the final expression for each sample matching to logFC of topTable. In Law et al(2016) paper, the v$E was considered as the final express ...
written 5 months ago by
zhouqz • 0
2
votes
1
answer
207
views
1
answer
... I am confused about the log2FC when I use the limma to analyze the RNA-seq data. In the paper (Law et al. 2016; https://f1000research.com/articles/5-1408 ), Log2FC of the gene (ENTREZID:12759) is -5.44 in basal.vs.lp, getting from topTable (Page 15). However, the mean expression getting from voom ...
Latest awards to zhouqz
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 16.09
Traffic: 267 users visited in the last hour