User: Cei Abreu-Goodger

Reputation:
830
Status:
Trusted
Location:
Mexico
Last seen:
4 years, 8 months ago
Joined:
12 years, 7 months ago
Email:
c**@langebio.cinvestav.mx

Posts by Cei Abreu-Goodger

<prev • 81 results • page 1 of 9 • next >
0
votes
1
answer
898
views
1
answer
camera.DGEList causes Error in qr.qty(QR, t(y)) : NA/NaN/Inf in foreign function call
... Dear Gordon, I've come across a problem with camera.DGEList() that seems related to extreme difference in counts between conditions. I have a very small example of my dataset that reproduces the problem, following this code: load(url("http://datos.langebio.cinvestav.mx/~cei/camera_problem.rdata")) ...
edger written 4.7 years ago by Cei Abreu-Goodger830 • updated 4.7 years ago by Aaron Lun25k
0
votes
5
answers
2.7k
views
5
answers
Comment: C: EdgeR: replicated pools, yes or not?
... Hi Ryan, I would like to pop in just to emphasize something about the current economics of sequencing that clearly depends on the lab or sequencing facility you're using. In our institute, and it sounds to me like Manuel is in a similar situation, the most expensive part of doing a proper RNA-seq ...
written 5.6 years ago by Cei Abreu-Goodger830
0
votes
1
answer
2.0k
views
1
answers
Comment: C: How to get sequences corresponding to a GRanges?
... Thanks Martin, that's exactly what I was looking for! (missed the showMethods("getSeq"), sorry) On 10/28/12 5:49 PM, Martin Morgan wrote: > On 10/28/2012 11:28 PM, Cei Abreu-Goodger wrote: >> Hello all, >> >> I was wondering if there was a simple way to get the sequences >& ...
written 7.0 years ago by Cei Abreu-Goodger830
2
votes
1
answer
2.0k
views
1
answer
How to get sequences corresponding to a GRanges?
... Hello all, I was wondering if there was a simple way to get the sequences corresponding to the ranges stored in a GRanges object. If you have the original sequences in a BSgenome object, you can use 'getSeq'. But what if you just have the fasta file, imported as a DNAStringSet object? I want to av ...
bsgenome written 7.0 years ago by Cei Abreu-Goodger830 • updated 7.0 years ago by Martin Morgan ♦♦ 24k
0
votes
1
answer
708
views
1
answers
Comment: C: edgeR, glmLRT error
... Dear Gordon, I've tried out the new code on a larger, also problematic, dataset and it works without any problems. Many thanks, Cei On 7/27/12 4:31 AM, Gordon K Smyth wrote: > Hi Cei, > > This is now fixed in edgeR 2.99.3 on Bioc-devel. Your example now runs > with the results given ...
written 7.3 years ago by Cei Abreu-Goodger830
0
votes
1
answer
708
views
1
answers
Comment: C: edgeR, glmLRT error
... Hi guys, Many thanks for the update, I'll check the devel in a few weeks. Best, Cei On 7/16/12 11:35 PM, Gordon K Smyth wrote: > Dear Cei, > > Thanks for the nice reproducible example. > > We have been working on a programming solution to eliminate this > occasionally occuring ...
written 7.3 years ago by Cei Abreu-Goodger830
0
votes
1
answer
708
views
1
answer
edgeR, glmLRT error
... Hi Gordon, I've been getting the following error upon running glmLRT: Error in beta[k, ] <- betaj[decr, ] NAs are not allowed in subscripted assignments which has previously been reported, for instance: https://stat.ethz.ch/pipermail/bioconductor/2011-February/038079.html I subsetted my c ...
written 7.3 years ago by Cei Abreu-Goodger830 • updated 7.3 years ago by Gordon Smyth39k
0
votes
2
answers
1.0k
views
2
answers
Comment: C: limma all adj.P.Val the same
... Dear all, In previous versions of R/BioC I was able to access the edgeR Users Guide from within R using the openVignette() function. Now this points to a brief vignette which only says that you see the edgeR User's Guide, but unlike the limmaUsersGuide() convenience function, edgeR doesn't provide ...
written 7.5 years ago by Cei Abreu-Goodger830
0
votes
1
answer
457
views
1
answers
Comment: C: question about the read.columns
... Check the read.table help (hint: check.names), which points you to the 'make.names' function... that's why. Cheers, Cei On 6/27/11 6:05 PM, Changbin Du wrote: > Hi, Valerie, > > Thanks for the reply! > > Yes, now I can successfully extract the columns I want with the required.col & ...
written 8.4 years ago by Cei Abreu-Goodger830
0
votes
0
answers
575
views
0
answers
beadarray: how to create BeadStudio output after createBeadSummaryData
... Hello, Is there a way of generating "BeadStudio like" files from within R? I have used beadarray to process raw Illumina output, obtaining an object of class 'ExpressionSetIllumina' using the functions readIllumina/backgroundCorrect/createBeadSummaryData. As far as I can see this is equivalent to ...
process beadarray arrayexpress written 8.8 years ago by Cei Abreu-Goodger830

Latest awards to Cei Abreu-Goodger

Popular Question 4.7 years ago, created a question with more than 1,000 views. For Does the strand of a microarray probe matter?
Popular Question 4.7 years ago, created a question with more than 1,000 views. For How to get sequences corresponding to a GRanges?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 338 users visited in the last hour