User: wariobrega

gravatar for wariobrega
wariobrega0
Reputation:
0
Status:
New User
Last seen:
2 years, 4 months ago
Joined:
3 years, 8 months ago
Email:
w*********@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 wariobrega

<prev • 6 results • page 1 of 1 • next >
0
votes
1
answer
823
views
1
answers
Comment: C: DESeq2: relevel contrasts after DESeq() has been called (time-course experiment
... Ok, I see your point. thanks for your time Mike!   Cheers,   D. ...
written 2.7 years ago by wariobrega0
0
votes
1
answer
823
views
1
answers
Comment: C: DESeq2: relevel contrasts after DESeq() has been called (time-course experiment
... Hi Mike,   Indeed, the modelling choices are many, as well as the biological assumptions. Here's an example of an MA plot of two stadium considering the LFC thrshold of 2 and showing fold change limits up to +/- 10: http://i.imgur.com/ZaitDHL.png . as you can see the distribution is quite scatte ...
written 2.7 years ago by wariobrega0
0
votes
1
answer
823
views
1
answers
Comment: C: DESeq2: relevel contrasts after DESeq() has been called (time-course experiment
... Hi Mike, Yes, I've made both a PCA plot and a clustering based on Poisson Distance. I will not post the cluistering because it is quite big (ith more than 100 samples would result unclear here) PCA: (I divided the embryo in 3 "substages" based on biological assumptions, as you can see here) http: ...
written 2.7 years ago by wariobrega0 • updated 2.7 years ago by Michael Love25k
1
vote
1
answer
823
views
1
answer
DESeq2: relevel contrasts after DESeq() has been called (time-course experiment of Drosophila development)
... Hello everyone! I'd like to pose a rather complicated question regarding a DE analysis I'm trying to do using DESeq2.   In brief, I have a dataset consisting of gene counts of d.melanogaster sampled at several time points and ranging all different development stages, from embryo to mature adult. ...
drosophila melanogaster deseq2 results multiple time points development written 2.7 years ago by wariobrega0 • updated 2.7 years ago by Michael Love25k
4
votes
2
answers
3.6k
views
2
answers
Questions regarding SVA batch effect normalizazion into DeSeq2 workflow
... Hello Everyone, I'm currently analyzing a series of RNA-Seq experiments that are splitted into 4 runs. In order to account for the batch effect of each experiments, I'm trying to correct my gene counts using sva, as recommended inside the Bioconductor RNASeq workflow (http://www.bioconductor.org/he ...
sva deseq2 batch effect written 3.6 years ago by wariobrega0 • updated 3.6 years ago by Michael Love25k
1
vote
1
answer
1.2k
views
1
answer
DESeq2 showing little if none significant DE genes (none if considering p-adj)
... Hello everyone, I'm Daniele, a junior researcher and former participant of the CSAMA event in 2015. After some month of waiting, I finally received my first RNA-Seq data, so I wanted to test DESeq2 to perform my DGE analysis. What I'm trying to do is to find differentially expressed features at ge ...
deseq2 multiple factor design written 3.7 years ago by wariobrega0 • updated 3.7 years ago by Michael Love25k

Latest awards to wariobrega

Popular Question 2.4 years ago, created a question with more than 1,000 views. For DESeq2 showing little if none significant DE genes (none if considering p-adj)
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Questions regarding SVA batch effect normalizazion into DeSeq2 workflow

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 476 users visited in the last hour