User: Victoria

gravatar for Victoria
Victoria0
Reputation:
0
Status:
New User
Last seen:
3 weeks, 1 day ago
Joined:
2 months ago
Email:
m********@yahoo.com

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

This helps us discourage the inappropriate use of our site.

Posts by Victoria

<prev • 9 results • page 1 of 1 • next >
0
votes
1
answer
131
views
1
answers
Comment: C: adjusting for confounding effects in edgeR
... Thanks a lot for your response and detailed explanation! ...
written 5 weeks ago by Victoria0
0
votes
1
answer
131
views
1
answers
Comment: C: adjusting for confounding effects in edgeR
... Thanks again for your response. I understand that the batch B is not useful, however we had to remove some other samples in this analysis (as the original study was different from this analysis). With this design, do you think additive model is enough for batch effect correction? How can I check m ...
written 5 weeks ago by Victoria0
0
votes
0
answers
66
views
0
answers
adding batch effects as a covariate in additive model in edgeR
... Hello everyone, I have RNA-Seq data from human tissues and I was wondering if I can add the batches in my additive model like this? (The batches are different dates of RNA extraction from tissue.) ``` x <- read.delim("rawCountMatrix.txt", row.names = "Gene") group <- factor(c(1,2,2,2,2,2,1 ...
edger batch effects written 6 weeks ago by Victoria0 • updated 6 weeks ago by James W. MacDonald50k
0
votes
1
answer
131
views
1
answers
Comment: C: adjusting for confounding effects in edgeR
... Thanks a lot for your reply Aaron, - Can I also add the batches in my additive model like this? (The batches are different dates of RNA extraction from tissue.) Batch <- factor(c("a","a","b","a","a","c","a","c","a","c")) design <- model.matrix(~group + Age + RIN + PMI + Batch) If yes, is ...
written 7 weeks ago by Victoria0
1
vote
1
answer
131
views
1
answer
adjusting for confounding effects in edgeR
... I have a set of RNA-Seq data from human tissue and want to compare the gene expression in cases and controls using EdgeR. If I want to adjust for the confounding effect of RIN, age and PMI; what is the correct way to do this? Here is my code: ``` library(edgeR) x <- read.delim("rawCountMatrix.tx ...
edger confounding written 8 weeks ago by Victoria0 • updated 8 weeks ago by Aaron Lun24k
0
votes
2
answers
383
views
2
answers
Comment: C: Confounded design, batch effect correction (edgeR)
... I have a similar question. I have a set of RNA-Seq data from human tissue and want to compare the gene expression in cases and controls using EdgeR. If I want to adjust for the confounding effect of RIN, age and PMI; what is the correct way to do this? Here is my code: library(edgeR) x <- read.d ...
written 8 weeks ago by Victoria0
0
votes
2
answers
383
views
2
answers
Comment: C: Confounded design, batch effect correction (edgeR)
... I have a similar question. I have a set of RNA-Seq data from human tissue and want to compare the gene expression in cases and controls using EdgeR. If I want to adjust for the confounding effect of RIN, age and PMI; what is the correct way to do this? Here is my code: library(edgeR) x <- read.d ...
written 8 weeks ago by Victoria0
0
votes
2
answers
383
views
2
answers
Comment: C: Confounded design, batch effect correction (edgeR)
... I have a similar question. I have a set of RNA-Seq data from human tissue and want to compare the gene expression in cases and controls using EdgeR. If I want to adjust for the confounding effect of RIN, age and PMI; what is the correct way to do this? Here is my code: library(edgeR) x <- read.d ...
written 8 weeks ago by Victoria0
0
votes
2
answers
383
views
2
answers
Answer: A: Confounded design, batch effect correction (edgeR)
... I have a similar question. I have a set of RNA-Seq data from human tissue and want to compare the gene expression in cases and controls using EdgeR. If I want to adjust for the confounding effect of RIN, age and PMI; what is the correct way to do this? Here is my code: library(edgeR) x <- read. ...
written 8 weeks ago by Victoria0

Latest awards to Victoria

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: 274 users visited in the last hour