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Forum: Bioinformatics 02-18-2019, 02:20 PM
Replies: 22
Views: 5,747
Posted By EVELE
Hi, Sorry for the resurrection of such old...

Hi,
Sorry for the resurrection of such old dialogues but I am quite confused.
I was thinking of doing a time-course analysis (as Assa did) having only 1 condition , 4 time points and 3 replicates...
Forum: RNA Sequencing 10-01-2015, 07:33 AM
Replies: 0
Views: 1,141
Posted By EVELE
DESeq2*: Dispersion in a DESeq analysis with design=~group

Hello,

I make a differential expression analysis between treated samples (factors) and untreated (controls) at different states (vegetative, early, inter, late).
The problem is that I lack...
Forum: RNA Sequencing 09-16-2015, 08:41 AM
Replies: 5
Views: 1,467
Posted By EVELE
In the manual link I sent, it goes like that: ...

In the manual link I sent, it goes like that:

Wald tests for the log2 fold changes at individual time points can be investigated using the test argument to results:

res30 <- results(ddsTC,...
Forum: RNA Sequencing 09-16-2015, 07:35 AM
Replies: 5
Views: 1,467
Posted By EVELE
Actually when you don't put test="Wald" I can see...

Actually when you don't put test="Wald" I can see that it is a LRT applied and we get LRT pvalues while when putting test="Wald" it is the Wald test pvalues we obtain.

I don't know which approach...
Forum: RNA Sequencing 09-16-2015, 07:15 AM
Replies: 5
Views: 1,467
Posted By EVELE
It is not the same. I can see differences when...

It is not the same.
I can see differences when I apply both ways to my data.

Common part of code:
> times=factor(c(1,rep(2,2),rep(3,2),0,1,rep(2,2),rep(3,2),0), levels=c(0,1,2,3))
> condition =...
Forum: RNA Sequencing 09-16-2015, 03:51 AM
Replies: 5
Views: 1,467
Posted By EVELE
Use of test="Wald" in the results of a time-course experiment

Hi all,

Concerning the example of the manual :
http://bioconductor.org/help/workflows/rnaseqGene/#time
in the "Time Course Experiments" paragraph,

library("fission")
data("fission")
ddsTC...
Forum: RNA Sequencing 08-24-2015, 06:46 AM
Replies: 0
Views: 1,060
Posted By EVELE
DESEQ2: Which of the following 2 contrast methods does what I want ?

Hi all,

I have 2 time course experiments.

For the first experiment I have 5 treated samples (1 for the vegetative stage with no replicates,
2 replicates for the early stage of autogamy and...
Forum: Bioinformatics 06-30-2015, 01:16 AM
Replies: 3
Views: 1,607
Posted By EVELE
Hi Michael, First of all many thanks for...

Hi Michael,

First of all many thanks for your prompt answer.
I tried to apply your suggestions.
As I am not sure for my understanding and the interpretations I give to my results, I expose (in...
Forum: Bioinformatics 06-26-2015, 02:12 AM
Replies: 3
Views: 1,607
Posted By EVELE
DESEQ2: How to use dispersion estimated from one dataset in another dataset

Hi all,

I have recently started using DeSeq2 and I would like to know if it is possible to do something like this:

I have 3 time course experiments (1 control and 2 treated (A and B)) but I do...
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