Moderator: Levi Waldron

gravatar for Levi Waldron
Levi Waldron600
Reputation:
600
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:
1 week ago
Joined:
9 years, 2 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 • 73 results • page 2 of 8 • next >
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Answer: A: help for package DESeq2 in R
... The error message seems clear: DESeq2 is intended for count data, and counts cannot be negative. You'll have to identify an appropriate statistical model and implementation for your data. This answer is necessarily vague because I don't know anything about your experiment or data. This online course ...
written 29 days ago by Levi Waldron600
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Comment: C: DESeq2 library loading error
... I'll just add: be sure to follow the instructions at www.bioconductor.org/install and use biocLite() to update your packages and to install new ones, including those from CRAN. Using any other method of installing and updating packages, such as install.packages() or RStudio's menus, introduces risk ...
written 4 weeks ago by Levi Waldron600
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Answer: A: DSEq2 error message at loading
... I noticed that DESeq2_1.20.0, DelayedArray_0.6.1, and SummarizedExperiment_1.10.1 are all in your namespace already. If you've updated some packages, perhaps try restarting your R session and reloading your libraries. ...
written 4 weeks ago by Levi Waldron600
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Answer: A: Handling pseudogenes in RNA-seq
... I can't advise on the biological advisability of this, but Bioconductor annotation packages do annotate pseudogene transcripts as well as gene transcripts: > library(EnsDb.Hsapiens.v86) > ts <- transcripts(EnsDb.Hsapiens.v86) > grep("pseudo", unique(ts$tx_biotype), val=TRUE) [1] "tran ...
written 4 weeks ago by Levi Waldron600
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Comment: C: how to add a new column in colData in SummarizedExperiment
... You can create your new colData any way you want, as long as 1) your replacement colData is still of class DataFrame, and 2) your replacement DataFrame still has rownames identical to the colnames of the SummarizedExperiment. Note you you could also construct a new SummarizedExperiment using the Sum ...
written 4 weeks ago by Levi Waldron600
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Answer: A: how to add a new column in colData in SummarizedExperiment
... Core Bioconductor classes like SummarizedExperiment are designed so you should not have to use @ to access slots directly, and users are encouraged instead to use the accessors / setters provided (discussion of why). I haven't tried to reproduce your steps, but here are a couple ways that appending ...
written 4 weeks ago by Levi Waldron600
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Comment: C: Differences between RTCGA and TCGAbiolinks data
... Indeed Marcin, my apologies! That explains how the asker was getting 2015-11-01 release data; they should be using your "20160128" set of data packages. ...
written 5 weeks ago by Levi Waldron600
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Comment: C: Genes listed in GO categories
... I was curious though about how 1) the number of Ensembl IDs is almost exactly a factor of 3 greater than the number of Entrez IDs, and 2) the over-representation p-values come out almost exactly the same. I suppose the factor of 3 is just a coincidence but I'm surprised the gene set size is so diffe ...
written 5 weeks ago by Levi Waldron600
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Comment: C: Differences between RTCGA and TCGAbiolinks data
... Hi Atakan, The last TCGA Firehose run date was 20160128, and there are no new cases or survival follow-up after that date. It’s that snapshot that RTCGAToolbox, TCGABiolinks, and curatedTCGAData can provide you with, and it’s the most recent data available from Firehose. curatedTCGAData does someth ...
written 5 weeks ago by Levi Waldron600
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Answer: A: Differences between RTCGA and TCGAbiolinks data
... Dear Atakan, I'm not sure why, but you're not getting the last follow-up from RTCGAToolbox, which I could see by comparing the follow-up times of patients who were alive at last follow-up. May I suggest making your life easier and using curatedTCGAData, which provides these data as MultiAssayExperi ...
written 5 weeks ago by Levi Waldron600

Latest awards to Levi Waldron

Scholar 3 months ago, created an answer that has been accepted. For A: Gene set enrichment analysis
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Reproducibility of MultiDataSet Comparison
Popular Question 2.3 years ago, created a question with more than 1,000 views. For multiple ColSideColors-type annotations on a heatmap
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
Scholar 3.6 years ago, created an answer that has been accepted. For A: Gene set enrichment analysis
Autobiographer 3.7 years ago, has more than 80 characters in the information field of the user's profile.

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