User: Alejandro Reyes

gravatar for Alejandro Reyes
Alejandro Reyes1.6k
Reputation:
1,610
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Trusted
Location:
Dana-Farber Cancer Institute, Boston, USA
Twitter:
@areyesq
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Last seen:
1 week, 3 days ago
Joined:
6 years, 8 months ago
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a*****************@gmail.com

Posts by Alejandro Reyes

<prev • 273 results • page 2 of 28 • next >
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Comment: C: DEXSeq time course design
... No problem! The "sample" column is normally a column in colData that is added by default when creating a DEXSeqDataSet object, if you don't have it you should add it. This is a term that accounts for sample-specific contributions, it also absorbs other effects such as changes in gene expression. Mor ...
written 4 months ago by Alejandro Reyes1.6k
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Answer: A: DEXSeq time course design
... Hi,  I think your reasoning of limiting only to samples with replicates is a great one.  The formulae that you are specifying might not be the correct ones for the hypothesis that you want to test.   For the question "Is there a difference in exon usage in each organ going from p3 up to p60", I t ...
written 4 months ago by Alejandro Reyes1.6k
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Comment: C: Need to read in DEXSeqResults object to R from csv
... Hi Christina, can you post the complete code that you are using along with the output of your sessionInfo()? ...
written 4 months ago by Alejandro Reyes1.6k
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Comment: C: Interaction effect sizes from DEXseq
... Hi Stuart. The four values would correspond to exon usage values after applying a variance stabilizing transformation. The exon fold changes are estimated from these values but before being variance-stabilized transformed, this is the reason why they can't be estimated from the four exon usage value ...
written 5 months ago by Alejandro Reyes1.6k
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Answer: A: Interaction effect sizes from DEXseq
... Hi Stuart, Thanks for your detailed post. Getting the "exon usage" fold change of an interaction term is currently not supported. However, you can visualize the effects of the interaction test by concatenating your two columns (mut and treat) in a single column and using the new column for estimateE ...
written 5 months ago by Alejandro Reyes1.6k
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News: Latin American BioC Developers Workshop 2018
... We are pleased to announce the Latin American Bioconductor Developers Workshop, which will take place in Cuernavaca, Mexico, from July 30th to August 3rd, 2018. The workshop is intended to encourage local R users, bioinformaticians and programmers to contribute packages to the Bioconductor project. ...
news bioc-devel bioconductor developers written 6 months ago by Alejandro Reyes1.6k
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Comment: C: DEXSeqHTML and biomart object
... Names are matched based on the rownames of extraCols. Thus, the rownames of extraCols should match what is stored in geneIDs().  Another minimal example: library(DEXSeq) data(pasillaDEXSeqDataSet, package="pasilla") dxr <- DEXSeq( dxd ) extraCols <- data.frame( ids=unique(geneIDs(dxd)), myg ...
written 6 months ago by Alejandro Reyes1.6k
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Comment: C: Annotation of DEXSeqHTML with biomaRt
... Not sure what is going wrong. Have you tried to include these names by doing the biomart call outside of DEXSeqHTML and then passing the data.frame (where the rownames are the `geneIDs()`) to the extraCols parameter? ...
written 6 months ago by Alejandro Reyes1.6k
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Comment: C: DEXSeq - dexseq_count.py issue
... I have been unable to solve this issue because I can't reproduce the error. But this might be a good start! Are you running the same versions of python and HTSeq through the command line and through Galaxy? ...
written 6 months ago by Alejandro Reyes1.6k
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Comment: C: DEXSeq - dexseq_count.py issue
... Sorry, I still can't reproduce the error message. How are you invoking the dexseq_count.py script? ...
written 7 months ago by Alejandro Reyes1.6k

Latest awards to Alejandro Reyes

Scholar 16 months ago, created an answer that has been accepted. For A: DEXSeqHTML and biomart object
Scholar 16 months ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Translating model formula from DESeq to DEXSeq
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: DEXSeq with mutliple experimental conditions - definig contrasts
Scholar 2.6 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 2.7 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 2.9 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 2.9 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 2.9 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: DEXSeq and Independent filtering
Scholar 2.9 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Centurion 3.8 years ago, created 100 posts.

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