User: candida.vaz

gravatar for candida.vaz
candida.vaz40
Reputation:
40
Status:
New User
Location:
Singapore
Last seen:
4 months ago
Joined:
4 years, 7 months ago
Email:
c**********@gmail.com

Posts by candida.vaz

<prev • 24 results • page 1 of 3 • next >
0
votes
1
answer
268
views
1
answers
Comment: C: Paired analysis setup using edgeR - follow up question
... Thanks a lot Aaron for the advice. I never came across the spline concept in the limma/edgeR guide. Could you please let me know where can I find it? I will be using the additivity assumption + Age in model.matrix() (understand that it may not be true in complex biological systems. Can I just c ...
written 4 months ago by candida.vaz40
0
votes
1
answer
268
views
1
answers
Comment: C: Paired analysis setup using edgeR - follow up question
... Thank you for your advice Aaron. Age of the patients don't change much except by a few months during the two visits. My concern is the effect of "Age" itself on the outcome. I am interested in removing the effect of Age or any such factor and seeing only the effect of Treatment on the outcome. S ...
written 4 months ago by candida.vaz40
0
votes
1
answer
268
views
1
answers
Comment: C: Paired analysis setup using edgeR - follow up question
... Dear Aaron, Just to follow up on the same analysis: was wondering if one could run the double voom and double duplicate correlation on a model that includes adjusting for confounding factors. For example if Age is a confounding factor then the design model will be: **design <- model.matrix( ~0 ...
written 4 months ago by candida.vaz40
0
votes
1
answer
268
views
1
answers
Comment: C: Paired analysis setup using edgeR - follow up question
... Dear Aaron, Thanks a ton for your suggestions! ...
written 5 months ago by candida.vaz40
0
votes
1
answer
268
views
1
answers
Comment: C: Paired analysis setup using edgeR - follow up question
... Thanks a ton Aaron! #1. To fuse into a single variable can I use: Group <- factor(paste(Categ, Visit, sep=".")) raw <- DGEList(counts=counts, group=Group) raw$samples <- cbind(raw$samples,Cid,Visit) (Where Categ =placebo/treatment & Visit=two time points) #2. For filtering (yo ...
written 5 months ago by candida.vaz40
0
votes
1
answer
268
views
1
answers
Comment: C: Paired analysis setup using edgeR - follow up question
... Dear Aaron, I had used limma voom with duplicateCorrelation blocking on id. This is my code...does this seem ok? or could you give your suggestions. ## Read in and annotate ## counts <- read.delim("all-samples.txt", row.names="Symbol", header = T) metrics <- read.delim("checking-metrics- ...
written 5 months ago by candida.vaz40
0
votes
1
answer
268
views
1
answers
Comment: C: Paired analysis setup using edgeR - follow up question
... Dear Aaron, Thank you so very much for the detailed explanation and solutions to my questions! So grateful! Regards, Candida ...
written 5 months ago by candida.vaz40
6
votes
1
answer
268
views
1
answer
Paired analysis setup using edgeR - follow up question
... Dear Bioconductor support team, This question is a follow up of the same I asked before, and then I carried out some analysis, but need help:- I have samples from two time points. The samples belong to two categories: Treatment and Placebo as follows: 005v1 Placebo 005v4 Placebo 008v1 Treat ...
edger written 5 months ago by candida.vaz40
0
votes
1
answer
215
views
1
answers
Comment: C: Setting up the design for paired analysis
... Thank you James for the suggestion, ...
written 5 months ago by candida.vaz40
1
vote
1
answer
215
views
1
answer
Setting up the design for paired analysis
... Dear Bioconductor support team, I have samples from two time points namely V1 and V4. The samples belong to two categories: Treatment and Placebo as follows: 005v1 Placebo 005v4 Placebo 008v1 Treatment 008v4 Treatment The ID number 005 etc represent the same sample at two time points. ...
limma edger paired design written 6 months ago by candida.vaz40

Latest awards to candida.vaz

Popular Question 4.1 years ago, created a question with more than 1,000 views. For Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Batch effect removal in edgeR
Great Question 4.1 years ago, created a question with more than 5,000 views. For Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
Popular Question 4.1 years ago, created a question with more than 1,000 views. For What are logCPM values in the Differentially Expressed Genes output
Epic Question 4.1 years ago, created a question with more than 10,000 views. For Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
Great Question 4.1 years ago, created a question with more than 5,000 views. For Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 269 users visited in the last hour