User: myprogramming2016

Reputation:
0
Status:
New User
Last seen:
2 years, 6 months ago
Joined:
3 years, 10 months ago
Email:
m****************@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 myprogramming2016

<prev • 34 results • page 2 of 4 • next >
0
votes
3
answers
525
views
3
answers
Answer: A: GO annotation and gene set testing for plant dataset
... Hi Aaron, I estimated homologous gene and GO annotation for each of the transcript using Arabidopsis genome. I am not clear with defining all transcripts belonging to a single GO term as a gene set. Could you please send me an example file and R code for roast and camera? Thanks for your help!   ...
written 3.5 years ago by myprogramming20160
0
votes
3
answers
525
views
3
answers
GO annotation and gene set testing for plant dataset
... Hi,  I am working on plant dataset which is a close relative of Arabidopsis.  I performed differential expression analysis using an edgeR and found significant DE genes. I would like to identify associated GO terms.  I have a transcript as a Scaffold, and not the ENTREZ ID.  I am just wondering w ...
annotation go topgo edger bioconductor written 3.5 years ago by myprogramming20160
0
votes
1
answer
605
views
1
answers
Comment: C: Interpreting contrasts in edgeR
... Thanks Ryan for the explanation. ...
written 3.6 years ago by myprogramming20160
1
vote
1
answer
605
views
1
answer
Interpreting contrasts in edgeR
... Hi, I have a question about interpreting contrast. I have three conditions, for e.g. high, med and low. I am interesting in looking at the genes which are differentially expressed in high condition over others. I am using following code to look at High vs Low HvsL<-makeContrasts(high - low,le ...
edger written 3.6 years ago by myprogramming20160 • updated 3.6 years ago by Ryan C. Thompson7.4k
0
votes
1
answer
955
views
1
answers
Comment: C: design matrix in GLM
... Thanks for your help. ...
written 3.7 years ago by myprogramming20160
0
votes
1
answer
955
views
1
answers
Comment: C: design matrix in GLM
... Thanks for your comments on the code. You mean I should use glmQLFit() instead of glmFit + glmLRT. I am not quite sure. Please guide me   fit <- glmQLFit(y, design, robust=TRUE)  qlf <- glmQLFTest(fit)  topTags(qlf) In addition, I would like to subset DE data using 5% FDR and log-fold ...
written 3.7 years ago by myprogramming20160
0
votes
1
answer
955
views
1
answers
Comment: C: design matrix in GLM
... Thanks Aaron. I checked both the designs. They are yielding similar output.  Secondly, I have seen in the example case studies in the edgeR manual that they have used glmQFit().  I am just wondering whether I should use glmFit() or glmQFit()?  How do I decide? I have data in three biological repl ...
written 3.7 years ago by myprogramming20160
5
votes
1
answer
955
views
1
answer
design matrix in GLM
... Hi, I am looking for differentially expressed genes between three different groups.  What is the preferred method of design matrix in GLM from the following?  design<-model.matrix(~0+group,data=y$samples)  or design<-model.matrix(~group,data=y$samples) Thanks       ...
edger written 3.7 years ago by myprogramming20160 • updated 3.7 years ago by Aaron Lun25k
0
votes
1
answer
1.2k
views
1
answers
Comment: C: Normalization in edgeR
... Thanks for your help. I have re-written the codes.  I would like to subset the read counts without converting them into CPM. I mean, subsetting for raw read counts. I am planning to use median method of normalization over TMM.  I want to subset for >10 counts and it should be present in atleast ...
written 3.8 years ago by myprogramming20160
2
votes
1
answer
1.2k
views
1
answer
Normalization in edgeR
... Hi, I am not quite clear about the normalization in edgeR. I am not seeing any change in the actual read counts. They are same numbers except filtered for >10 reads, library size is reduced and norm.factor is 1. Could you please comments on this? Codes: x<-read.delim("counts.txt",header=T ...
rnaseq edger bioconductor written 3.8 years ago by myprogramming20160 • updated 3.8 years ago by Gordon Smyth39k

Latest awards to myprogramming2016

Popular Question 2.5 years ago, created a question with more than 1,000 views. For summaries featureCounts output for egeR
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Normalization in edgeR
Popular Question 2.5 years ago, created a question with more than 1,000 views. For threshold to filter lowly expressed genes

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 152 users visited in the last hour