User: candida.vaz

gravatar for candida.vaz
candida.vaz40
Reputation:
40
Status:
New User
Location:
Singapore
Last seen:
7 months, 4 weeks ago
Joined:
4 years, 11 months ago
Email:
c**********@gmail.com

Posts by candida.vaz

<prev • 24 results • page 1 of 3 • next >
0
votes
1
answer
370
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 8 months ago by candida.vaz40
0
votes
1
answer
370
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 8 months ago by candida.vaz40
0
votes
1
answer
370
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 8 months ago by candida.vaz40
0
votes
1
answer
370
views
1
answers
Comment: C: Paired analysis setup using edgeR - follow up question
... Dear Aaron, Thanks a ton for your suggestions! ...
written 9 months ago by candida.vaz40
0
votes
1
answer
370
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 9 months ago by candida.vaz40
0
votes
1
answer
370
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 9 months ago by candida.vaz40
0
votes
1
answer
370
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 9 months ago by candida.vaz40
6
votes
1
answer
370
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 9 months ago by candida.vaz40
0
votes
1
answer
292
views
1
answers
Comment: C: Setting up the design for paired analysis
... Thank you James for the suggestion, ...
written 9 months ago by candida.vaz40
1
vote
1
answer
292
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 10 months ago by candida.vaz40

Latest awards to candida.vaz

Great Question 4.4 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
Epic Question 4.4 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
Popular Question 4.4 years ago, created a question with more than 1,000 views. For What are logCPM values in the Differentially Expressed Genes output
Great Question 4.4 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 4.4 years ago, created a question with more than 1,000 views. For Batch effect removal in edgeR
Popular Question 4.4 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 186 users visited in the last hour