User: Alejandro Reyes

gravatar for Alejandro Reyes
Alejandro Reyes1.6k
Reputation:
1,550
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Location:
Dana-Farber Cancer Institute, Boston, USA
Twitter:
@areyesq
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Google Scholar Page
Last seen:
6 hours ago
Joined:
6 years, 5 months ago
Email:
a*****************@gmail.com

Posts by Alejandro Reyes

<prev • 269 results • page 1 of 27 • next >
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Comment: C: DEXSeq: Error running dexseq_prepare_annotation.py
... Thanks for the details. I could reproduce the error message using python 3.6 and HTSeq 0.10.0: I think it is a bug in HTSeq. I'll report this to the maintainers of HTSeq. While this gets fixed, I would recommend  using python 2.7.  Alejandro ps. just uploaded the resulting file here: https://www.d ...
written 6 hours ago by Alejandro Reyes1.6k
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Comment: C: DEXSeq: Error running dexseq_prepare_annotation.py
... I just ran the following without problems using python 2.7.10 and HTSeq 0.6.1p1: curl -o Homo_sapiens.GRCh37.87.gtf.gz ftp://ftp.ensembl.org/pub/grch37/update/gtf/homo_sapiens//Homo_sapiens.GRCh37.87.gtf.gz gunzip Homo_sapiens.GRCh37.87.gtf.gz python ~/Work/Rpcks/DEXSeq/inst/python_scripts/dexseq_p ...
written 11 hours ago by Alejandro Reyes1.6k
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Comment: C: DEXSeq: Error running dexseq_prepare_annotation.py
... Oh I see, sorry I did not catch that earlier. Could you point me to the link to the gtf file that you are using? ...
written 11 hours ago by Alejandro Reyes1.6k
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Comment: C: DEXSeq: Error running dexseq_prepare_annotation.py
... Hi Suzanne, have you checked if there are gene identifiers that appear in multiple chromosomes? ...
written 11 hours ago by Alejandro Reyes1.6k
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Answer: A: DEXSeq: Error running dexseq_prepare_annotation.py
... Hi Suzanne,  The error message indicates that the same gene ID was found in two different chromosomes. As you suspect this is likely an error in the annotation file. The easiest solution is to remove that gene identifier from the gtf file.  Best regards, Alejandro ...
written 21 hours ago by Alejandro Reyes1.6k
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Answer: A: DEXseq with technical replicates
... Hi g.e.novakowsky,  The DEXSeq model considers two sources of variation, (1) biological, which is estimated from biological replicates and (2) technical, which is small compared to biological variability, follows a Poisson distribution and can be estimated directly from the mean (see for example: h ...
written 11 days ago by Alejandro Reyes1.6k
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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 5 weeks 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 5 weeks 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 5 weeks 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 8 weeks ago by Alejandro Reyes1.6k

Latest awards to Alejandro Reyes

Scholar 13 months ago, created an answer that has been accepted. For A: DEXSeqHTML and biomart object
Scholar 13 months ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Translating model formula from DESeq to DEXSeq
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: DEXSeq with mutliple experimental conditions - definig contrasts
Scholar 2.3 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 2.5 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 2.6 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
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
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: DEXSeq and Independent filtering
Scholar 2.7 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Centurion 3.5 years ago, created 100 posts.

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