User: Alejandro Reyes

gravatar for Alejandro Reyes
Alejandro Reyes1.5k
Reputation:
1,460
Status:
Trusted
Location:
Dana-Farber Cancer Institute, Boston, USA
Twitter:
@areyesq
Scholar ID:
Google Scholar Page
Last seen:
1 week, 2 days ago
Joined:
5 years, 9 months ago
Email:
a*****************@gmail.com

Posts by Alejandro Reyes

<prev • 247 results • page 2 of 25 • next >
0
votes
2
answers
216
views
2
answers
Answer: A: Sample label swap in HTML results
... Hi Maximino. Thanks for sending your files. I think the the sample swap is in your code. Specifically the line below is not returning the tabular files in the same order as you are specifying  list.files(full.names=TRUE,pattern=".tabular") [1] "./AS4_DEXSeq.tabular" "./BD1_DEXSeq.tabular" "./ ...
written 4 months ago by Alejandro Reyes1.5k
0
votes
2
answers
216
views
2
answers
Comment: C: Sample label swap in HTML results
... alejandro.reyes.ds at gmail please! ...
written 4 months ago by Alejandro Reyes1.5k
0
votes
2
answers
216
views
2
answers
Comment: C: Sample label swap in HTML results
... I see... in that case my previous explanation is not valid. But still, I can't reproduce these results. Would you mind sending me your raw files so I can try to reproduce the swap? Alejandro  ...
written 4 months ago by Alejandro Reyes1.5k
0
votes
2
answers
216
views
2
answers
Comment: C: Sample label swap in HTML results
... From the raw count matrix that you posted, you will see that the counts for the controls are generally higher than the resistant samples (not only for exons 38 and 39, but for all exons). Once you normalize for sequencing depth, the counts for the resistant samples are higher than in the resistant s ...
written 4 months ago by Alejandro Reyes1.5k
0
votes
2
answers
216
views
2
answers
Comment: C: Sample label swap in HTML results
... I believe the answer is there: the samples are not swapped. The count matrix that you are showing is not normalized for sequencing depth. If you do normalize for sequencing depth, you should get consistent values to the normalized counts plot. counts(dxd, normalized=TRUE)   ...
written 4 months ago by Alejandro Reyes1.5k
0
votes
2
answers
216
views
2
answers
Comment: C: Sample label swap in HTML results
... Sorry for not being clear. Could you post the plot resulting from the following line of code? plotDEXSeq( dxr1, "ENSG00000006576.16", norCounts=TRUE, legend=TRUE, cex.axis=1.2, cex=1.3, lwd=2 ) ...
written 4 months ago by Alejandro Reyes1.5k
0
votes
2
answers
179
views
2
answers
Comment: C: Unusually long running times for getMeth function since latest release
... Your fix worked for me as well - Thanks a lot! ...
written 4 months ago by Alejandro Reyes1.5k
0
votes
2
answers
216
views
2
answers
Comment: C: Sample label swap in HTML results
... Hi Maximino. I made a couple of tests and I could not reproduce the sample swap that you mentioned. Sorry for the multiple request, but could you include the normalized counts (norCounts) in the plotDEXSeq function? ...
written 4 months ago by Alejandro Reyes1.5k
0
votes
2
answers
179
views
2
answers
Comment: C: Unusually long running times for getMeth function since latest release
... Thanks Peter and Kasper! Peter, if you need a reproducible example (object + code) as Kasper suggested, let me know and I would be happy to provide one. Alejandro ...
written 4 months ago by Alejandro Reyes1.5k
0
votes
2
answers
216
views
2
answers
Comment: C: Sample label swap in HTML results
... Could you also the output of your sessionInfo() please? ...
written 4 months ago by Alejandro Reyes1.5k

Latest awards to Alejandro Reyes

Scholar 20 months ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 21 months ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 24 months ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 24 months ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 2.0 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: DEXSeq and Independent filtering
Scholar 2.0 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Centurion 2.8 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 153 users visited in the last hour