Moderator: Levi Waldron

gravatar for Levi Waldron
Levi Waldron790
Reputation:
790
Status:
Trusted
Location:
CUNY Graduate School of Public Health and Health Policy, New York, NY
Website:
http://www.waldronlab.io/
Twitter:
leviwaldron1
Scholar ID:
Google Scholar Page
Last seen:
6 days, 19 hours ago
Joined:
9 years, 6 months ago
Email:
l****************@gmail.com

I'm an assistant professor of biostatistics at the CUNY Graduate School of Public Health and Health Policy in New York City, and have a special interest in streamlining the analysis of publicly available cancer genomics data in Bioconductor.  I maintain the curatedOvarianData, ffpe, and ffpeExampleData Bioconductor packages, and was closely involved with the creation of curatedCRCData, curatedBladderData, and simulatorZ.  I also maintain a couple CRAN packages: HGNChelper and pensim.  I'm involved in the development of curated data resources and methods for the analysis of multi-assay genomic experiments such as TCGA in Bioconductor (https://github.com/waldronlab/biocMultiAssay).

Posts by Levi Waldron

<prev • 88 results • page 1 of 9 • next >
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News: BioC2019 June 24-27 in New York City
... Mark your calendars for the BioC2019 Bioconductor annual conference in Manhattan, New York City (Twitter: #BioC2019). Developer Day is June 24 at NYU Langone Medical Center, the User Conference is June 25-26 at The Rockefeller University, and there will be a special one-time-only "Robert Gentleman S ...
news conference written 20 days ago by Levi Waldron790
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Comment: C: MultiAssayExperiment: Error in dimnames(x) <- dn : length of 'dimnames' [2] not
... You can check in devel at http://bioconductor.org/packages/devel/bioc/html/MultiAssayExperiment.html (no it isn't), but if you want it immediately you can install directly from GitHub: BiocManager::install("waldronlab/MultiAssayExperiment") It should propagate to devel by tomorrow. ...
written 7 weeks ago by Levi Waldron790
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Comment: C: MultiAssayExperiment: Error in dimnames(x) <- dn : length of 'dimnames' [2] not
... Sorry I made a wrong statement before: the second position of square bracket subsetting acts on the rows of `colData` of your MultiAssayExperiment, not directly on the experimental data matrix columns. But I'm afraid I won't be able to figure out what's going on for you without a reproducible exampl ...
written 7 weeks ago by Levi Waldron790
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Comment: C: MultiAssayExperiment: Error in dimnames(x) <- dn : length of 'dimnames' [2] not
... Actually, can I request that you first do your subsetting alone in a step, before trying wideFormat()? I see that you are attempting to select columns (1:108) that do not exist in some of your experiments (three have only 65 columns), which is likely the cause of your error. ...
written 7 weeks ago by Levi Waldron790
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Comment: C: MultiAssayExperiment: Error in dimnames(x) <- dn : length of 'dimnames' [2] not
... This sounds like a corner case that we'll need to have either the object itself or reproducible code that generates it, in order to debug. Would appreciate that very much if you can provide it. ...
written 7 weeks ago by Levi Waldron790
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Comment: C: MultiAssayExperiment: how can i change name of a experiment in a multiassayexper
... You would have to use the development version of Bioconductor to get this update before the next release (which will happen in October): http://bioconductor.org/developers/how-to/useDevel/ ...
written 9 weeks ago by Levi Waldron790
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Comment: C: MultiAssayExperiment: how can i change name of a experiment in a multiassayexper
... That's great, Marcel. Nice feature addition.  ...
written 9 weeks ago by Levi Waldron790
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Comment: C: MultiAssayExperiment: how can i change name of a experiment in a multiassayexper
... Marcel has provided the real solution to your request below - thanks for the feature request! But if you are using bioc-release and just want a hack in the meantime, here it is. The error you saw was due to trying to subset to an experiment that doesn't exist, it isn't related to wideFormat(). See t ...
written 9 weeks ago by Levi Waldron790
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Comment: C: MultiAssayExperiment: how can i change name of a experiment in a multiassayexper
... > > when i try to generate wideFormat: > > > wideFormat(mae2[ , , c("exp_3")] > > Error: subscript contains invalid rownames > > Any idea? > I don't think you have renamed the experiment, and you don't have one named exp_3. I'm not at a computer but will give a more com ...
written 9 weeks ago by Levi Waldron790
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Answer: A: MultiAssayExperiment: how can i change name of a experiment in a multiassayexper
... There's currently no direct way to rename an ExperimentList slot, because the sampleMap would have to be modified simultaneously. One hack would be to use the `c()` function to concatenate a new ExperimentList element, then subset to remove the old one. I'm not sure if this is a common enough use ca ...
written 9 weeks ago by Levi Waldron790

Latest awards to Levi Waldron

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Error creating DESeqDataSet from "airway" SummarizedExperiment
Appreciated 6 weeks ago, created a post with more than 5 votes. For BioC2019 June 24-27 in New York City
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Reproducibility of MultiDataSet Comparison
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
Supporter 5 months ago, voted at least 25 times.
Scholar 5 months ago, created an answer that has been accepted. For A: Gene set enrichment analysis
Popular Question 5 months ago, created a question with more than 1,000 views. For multiple ColSideColors-type annotations on a heatmap
Scholar 7 months ago, created an answer that has been accepted. For A: Gene set enrichment analysis
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Reproducibility of MultiDataSet Comparison
Popular Question 2.6 years ago, created a question with more than 1,000 views. For multiple ColSideColors-type annotations on a heatmap
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
Scholar 4.0 years ago, created an answer that has been accepted. For A: Gene set enrichment analysis
Autobiographer 4.0 years ago, has more than 80 characters in the information field of the user's profile.

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