User: Alejandro Reyes

gravatar for Alejandro Reyes
Alejandro Reyes1.5k
Reputation:
1,480
Status:
Trusted
Location:
Dana-Farber Cancer Institute, Boston, USA
Twitter:
@areyesq
Scholar ID:
Google Scholar Page
Last seen:
1 week ago
Joined:
5 years, 11 months ago
Email:
a*****************@gmail.com

Posts by Alejandro Reyes

<prev • 248 results • page 1 of 25 • next >
0
votes
1
answers
122
views
1
answers
Answer: A: DEXSeqHTML and biomart object
... Hi! The easiest way to do that would be something along these lines:   library(DEXSeq) library(biomaRt) data("pasillaDEXSeqDataSet", package="pasilla") dxr <- DEXSeq( dxd ) mart <- useMart( biomart="ensembl", dataset="dmelanogaster_gene_ensembl" ) extraCols <- getBM(attributes=c("ensem ...
written 6 weeks ago by Alejandro Reyes1.5k
0
votes
0
answers
113
views
0
answers
Comment: C: DEXSeq Count files do not correspond to the flattened annotation file
... Uff, sorry for the delay: I missed your message earlier. I hope this has been solved. If not, could you check if the number of lines on your count files corresponds to the number of lines contatining "exonic_part" in the third column of your annotation file? ...
written 10 weeks ago by Alejandro Reyes1.5k
0
votes
0
answers
105
views
0
answers
bnbc: Does it makes sense to make batch effect correction optional?
... Thanks for developing bnbc! I am interested in using the proposed across sample normalization method (smoothing + per-band quantile normalization). However, my data was processed in a single batch and thus the batch correction step might not be needed. In the current implementation, I did not find a ...
bnbc written 10 weeks ago by Alejandro Reyes1.5k
0
votes
0
answers
190
views
0
answers
Comment: C: DEXSeq error with estimateExonFoldChanges
... Thanks for adding this. Your note on the sample size makes me think that the problem could be related to RAM usage. What kind of computer are you using? ...
written 3 months ago by Alejandro Reyes1.5k
0
votes
1
answers
106
views
1
answers
Answer: A: Algorithm behind splice=TRUE in DEXSeq
... Hi, the details of the estimation of exon fold changes is described in the DEXSeq paper. The "overall gene expression" can not be extracted from the DEXSeq results, but if you are interested in changes in gene expression it is better to look at packages like DESeq2, etc. I have not done a very syst ...
written 3 months ago by Alejandro Reyes1.5k
0
votes
0
answers
190
views
0
answers
Comment: C: DEXSeq error with estimateExonFoldChanges
... Can you update both R and Bioconductor at least to the latest release versions? If the error still occurs, could you please include the code that reproduces the error messages? ...
written 4 months ago by Alejandro Reyes1.5k
0
votes
0
answers
190
views
0
answers
Comment: C: DEXSeq error with estimateExonFoldChanges
... Hi Chen,  Have you tried to specify a smaller number of workers? Alejandro ...
written 4 months ago by Alejandro Reyes1.5k
0
votes
1
answers
351
views
1
answers
Answer: A: DEXSeqHTML Error on condition variable
... Hi mittjohns,  The parameter fitExpToVar of the function DEXSeqHTML requires a variable of the experiment that you are analyzing (it has the value "condition" by default but in your dataset that could be either "Genotype" or "Treatment").  However, this won't be useful to visualize the interaction ...
written 4 months ago by Alejandro Reyes1.5k
0
votes
0
answers
579
views
0
answers
Comment: C: DEXseq plot, determin the EU Fold change
... Hi, currently there is not a parameter for this, but I can add that to my todo list. In the meantime, what you could do is to set the adjusted p-values to 1 whenever the fold changes are lower than your threshold (only for the purposes of visualization).  ...
written 5 months ago by Alejandro Reyes1.5k
0
votes
0
answers
587
views
0
answers
Comment: C: Proper dataset form and model for DEXeq analysis
... Hi Heikki, could you include the output of as.data.frame( colData(dxd) ) ? Alejandro ...
written 5 months ago by Alejandro Reyes1.5k

Latest awards to Alejandro Reyes

Scholar 22 months ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 23 months ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 2.1 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 2.2 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 2.2 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: DEXSeq and Independent filtering
Scholar 2.2 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Centurion 3.0 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: 264 users visited in the last hour