The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

User: rodrigo.duarte88

Reputation:
0
Status:
New User
Last seen:
3 days, 22 hours ago
Joined:
7 months, 3 weeks ago
Email:
r***************@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 rodrigo.duarte88

<prev • 11 results • page 1 of 2 • next >
0
votes
1
answer
1.3k
views
1
answers
Comment: C: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
... I had the same error, and removing low count genes from counts table (as suggested in sva tutorial, https://bioconductor.org/packages/release/bioc/vignettes/sva/inst/doc/sva.pdf) worked for me. ...
written 18 days ago by rodrigo.duarte880
0
votes
0
answers
67
views
0
answers
Comment: C: Using PEER to identify hidden confounders in RNA-seq data (not working)
... Oops, sorry about that! To be fair, I think am going to try "sva", looks like there's more documentation for that one. Thanks, Martin! ...
written 23 days ago by rodrigo.duarte880
0
votes
1
answer
74
views
1
answers
Comment: C: How to calculate overlap between transposable elements differentially expressed
... Fantastic! Thanks, Michael! Just one more quick question (for peace of mind): I am using the "~1" design to create this dds object to extract the normalised counts, since I have no groups, right? ...
written 23 days ago by rodrigo.duarte880
0
votes
0
answers
67
views
0
answers
Using PEER to identify hidden confounders in RNA-seq data (not working)
... Hi all, I am trying to use PEER in R (on conda) to identify hidden confounders in the raw counts of my RNA-seq experiment. I am following their tutorial ( https://github.com/PMBio/peer/wiki/Tutorial ), but without much luck, and there's not much help available unfortunately. Anyone used this tool b ...
differential expression rna-seq peer hidden confounders written 23 days ago by rodrigo.duarte880 • updated 23 days ago by Martin Morgan ♦♦ 22k
0
votes
1
answer
72
views
1
answers
Comment: C: Handling missing data, DESeq2
... Looks like you have 3 time points, but how many samples for each time point do you have? I think that as long as you have at least 3 samples per time point, you should be fine? ...
written 24 days ago by rodrigo.duarte880
2
votes
1
answer
74
views
1
answer
How to calculate overlap between transposable elements differentially expressed in one experiment, with those expressed in another set of samples?
... Dear all, I've got a naive question for you, and I would really appreciate your thoughts. I found some transposable elements (TE) that were differentially expressed in a certain tissue, based on a case-control analysis of RNA-seq data using DESeq2, and a custom-made annotation for TEs. Now, **I w ...
deseq2 enrichment rna-seq gene expression written 24 days ago by rodrigo.duarte880 • updated 24 days ago by Michael Love21k
0
votes
1
answer
315
views
1
answers
Comment: C: Subsetting a tximport object
... Many thanks, Michael! This is super useful, as usual! ...
written 5 weeks ago by rodrigo.duarte880
0
votes
1
answer
315
views
1
answers
Comment: C: Subsetting a tximport object
... Hi [James][1], I was wondering if you know how I could remove samples from the tximport object which are contained in a list of outliers? Thanks! [1]: https://support.bioconductor.org/u/5106/ ...
written 5 weeks ago by rodrigo.duarte880
0
votes
1
answer
102
views
1
answers
Comment: C: DESeq2 - assessing expression of low count genes
... Thank you Michael! This is super helpful!    ...
written 11 weeks ago by rodrigo.duarte880
1
vote
1
answer
102
views
1
answer
DESeq2 - assessing expression of low count genes
... Hi all I've used an unpublished pipeline developed by collaborators to obtain raw counts of human endogenous retroviruses (HERVs) in RNA-seq data. I have control (CTRL; n= 279) and cases (n=259) which I want to test for differential HERV expression ("Profile") whilst covarying for the effect of ins ...
deseq2 low counts hervs prefiltering dispersion estimates written 12 weeks ago by rodrigo.duarte880 • updated 11 weeks ago by Michael Love21k

Latest awards to rodrigo.duarte88

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 187 users visited in the last hour