Admin: Marcel Ramos

gravatar for Marcel Ramos
Marcel Ramos ♦♦ 210
Reputation:
210
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Trusted
Location:
United States
Last seen:
2 days, 13 hours ago
Joined:
3 years, 6 months ago
Email:
m***********@roswellpark.org

Posts by Marcel Ramos

<prev • 36 results • page 1 of 4 • next >
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Comment: C: Simplifying a RaggedExperiment using qreduceAssay and weighted means.
... Hey all, How does this commit look? https://github.com/Bioconductor/RaggedExperiment/commit/9fdcfbf0779d3508af7ae0afc288f946758b60d6 Thanks, Marcel ...
written 5 weeks ago by Marcel Ramos ♦♦ 210
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Comment: C: TCGAutils: Error in .checkBarcodes(barcodes) : barcode delimiters not consistent
... Hi Mario, I've checked this with the Bioconductor release version 3.7 and it works as well. There may be something wrong with your installation. Check that you're not mixing versions of packages. Remove a couple of packages: remove.packages(c("BiocManager", "BiocVersion")). Your biocLite("BiocUp ...
written 7 weeks ago by Marcel Ramos ♦♦ 210
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Answer: A: TCGAutils: Error in .checkBarcodes(barcodes) : barcode delimiters not consistent
... Hi Mario, Can you please include your sessionInfo() ? This works for me with Bioc-devel 3.8. library(curatedTCGAData) library(TCGAutils) coad <- curatedTCGAData("COAD", "CN*", FALSE) sampleTables(coad) > sampleTables(coad) $`COAD_CNASeq-20160128` 01 10 11 68 55 13 $`COAD_CNASNP-201601 ...
written 7 weeks ago by Marcel Ramos ♦♦ 210
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Comment: C: Querying specific TCGA datasets through the MultiAssayExperiment R package
... 2) Yes, `curatedTCGAData` returns a `MultiAssayExperiment` data object. ...
written 7 weeks ago by Marcel Ramos ♦♦ 210
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Answer: A: How do you run BiocCheck from a continuous integration service?
... Hi all, I've looked into the issue and decided to contribute some code to add BiocCheck to the Travis-CI builder. I was finally able to get my code merged and to run a package check with BiocCheck. Interestingly, my package is producing a false positive with BiocCheck but the build is not erroring o ...
written 7 weeks ago by Marcel Ramos ♦♦ 210
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Answer: A: Querying specific TCGA datasets through the MultiAssayExperiment R package
... Hi Efstathios-Iason, 1) As you may be aware, there are quite a number of resources for accessing TCGA data. I would first point you to the curatedTCGAData Bioconductor package. This will give you access to COAD data as MultiAssayExperiment objects. You could also use curatedCRCData but you'd have ...
written 7 weeks ago by Marcel Ramos ♦♦ 210
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Comment: C: Retrieve accurate tumor stage data with TCGAbiolinks
... Hi Benjamin, It would be good to have Tiago Silva's input on this. It seems like, at least for this case, the curation process considered the TNM stages and coded for Stage IV Here are a few other resources that you can use to check these variables (many of which yield NA for pathologic_stage): Geno ...
written 3 months ago by Marcel Ramos ♦♦ 210
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Answer: A: Error while getFirehoseData of RTCGAToolbox package
... Hi Ankita, I was unable to reproduce the error. I suspect that it may have something to do with your internet connection.  Please check your connection settings and make sure that a firewall or VPN is not preventing you from accessing the remote file.  There are other known issues for users of Wi ...
written 4 months ago by Marcel Ramos ♦♦ 210
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Comment: C: R_Granges_adding merged Metadata columns
... Hi Melissa, Without a reproducible example, there is not much specific help that fellow Bioconductor users can provide. If you have the ranges of those variants that have been merged, you can use findOverlaps to find the overlapping ranges in the original GRanges that correspond to those variant acc ...
written 4 months ago by Marcel Ramos ♦♦ 210
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Comment: C: Error while uploading Bioconductor packages - R Shiny
... Hi Lloyd,  Thanks for posting a solution!  Best regards, Marcel  ...
written 4 months ago by Marcel Ramos ♦♦ 210

Latest awards to Marcel Ramos

Supporter 12 weeks ago, voted at least 25 times.
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Querying specific TCGA datasets through the MultiAssayExperiment R package
Scholar 14 months ago, created an answer that has been accepted. For A: Classes and methods for working with segmented copy number data
Scholar 16 months ago, created an answer that has been accepted. For A: Classes and methods for working with segmented copy number data
Scholar 16 months ago, created an answer that has been accepted. For A: Classes and methods for working with segmented copy number data

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