User: aec

gravatar for aec
aec40
Reputation:
40
Status:
New User
Location:
Last seen:
1 month ago
Joined:
2 years, 10 months ago
Email:
a**********@cnag.crg.eu

Posts by aec

<prev • 67 results • page 1 of 7 • next >
0
votes
1
answers
136
views
1
answers
Comment: C: time series, block by patient, between and within comparisons limma-voom
... Thanks Aaron, it worked perfectly. Now if I am interested in applying LRT method to detect differential genes between the two time-courses over time, how to set up the model with limma? 5 time-points is enough for using splines? ...
written 5 weeks ago by aec40
0
votes
1
answers
136
views
1
answers
Comment: C: time series, block by patient, between and within comparisons limma-voom
... Yes, irrespective of the group. ...
written 8 weeks ago by aec40
0
votes
1
answers
136
views
1
answers
Comment: C: time series, block by patient, between and within comparisons limma-voom
... I have 5 time points per patient, in total 15 patients. These 15 patients can be further divided in two groups for question b) ...
written 8 weeks ago by aec40
0
votes
1
answers
136
views
1
answers
Comment: C: time series, block by patient, between and within comparisons limma-voom
... sure, I will edit my post. ...
written 8 weeks ago by aec40
1
vote
1
answer
136
views
1
answer
time series, block by patient, between and within comparisons limma-voom
... Dear all, I have a time course RNA-seq analysis with the following design: 5 time points, 15 patients, 2 types of patients. the questions I would like to answer: a) expression differences across time points irrespective of patient type (t1 vs t2, t1 vs t3, ...) b) expression differences between ...
rna-seq patient limma-voom time series written 8 weeks ago by aec40 • updated 8 weeks ago by Aaron Lun21k
0
votes
0
answers
162
views
0
answers
Comment: C: differential expression analysis with big dataset and >500 surrogate variables
... thanks Michael.  ...
written 6 months ago by aec40
0
votes
0
answers
162
views
0
answers
Comment: C: differential expression analysis with big dataset and >500 surrogate variables
... n.sv <- num.sv(dat,mod) n.sv [1] 1   ...
written 6 months ago by aec40
0
votes
0
answers
162
views
0
answers
Comment: C: differential expression analysis with big dataset and >500 surrogate variables
... dds <- estimateSizeFactors(dds) dat <- counts(dds, normalized=TRUE) idx <- rowMeans(dat) > 1 dat <- dat[idx,] mod <- model.matrix(~case, colData(dds)) mod0 <- model.matrix(~1, colData(dds)) n.sv <- num.sv(dat,mod,method="leek") n.sv [1] 589   ...
written 6 months ago by aec40
1
vote
0
answers
162
views
0
answers
differential expression analysis with big dataset and >500 surrogate variables
... dear all, I have more than 500 RNA-seq samples and have to compare cases vs controls. I first run SVA to remove unknown variation and found >500 surrogate variables. Is a good practice to perform a LRT test with deseq2 where full model =~case+SV1+SV2+SVn and reduced model=~case to know how many ...
sva deseq2 differential expression lrt written 6 months ago by aec40
0
votes
1
answers
151
views
1
answers
Comment: C: interaction model deseq2 specific DE genes
... ok Michael, so none of this contrasts answer my question directly right? res = results(dds, contrast=c("temp","temp24",temp"21")) res = results(dds, name="strain2.temp24") res = results(dds, name="strain3.temp24") res = results(dds, contrast=list("strain3.temp24", "strain2.temp24")) ...
written 6 months ago by aec40

Latest awards to aec

Popular Question 8 weeks ago, created a question with more than 1,000 views. For order of covariates for GLM with edgeR
Popular Question 17 months ago, created a question with more than 1,000 views. For limma - complex design with paired samples, sex and batch effect

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 245 users visited in the last hour