User: Levi Waldron

gravatar for Levi Waldron
Levi Waldron380
Reputation:
380
Status:
Trusted
Location:
CUNY Graduate School of Public Health and Health Policy, New York, NY
Website:
http://www.waldronlab....
Twitter:
leviwaldron1
Scholar ID:
Google Scholar Page
Last seen:
1 month ago
Joined:
8 years, 6 months ago
Email:
l****************@gmail.com

I'm an assistant professor of biostatistics at the CUNY School of Public Health 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 • 44 results • page 1 of 5 • next >
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Answer: A: Reproducibility of MultiDataSet Comparison
... Also, I'm quite proud of the internal graph representation of the specimen:assay relationships (sampleMap(MAE)). It's a novel approach to maintaining consistency between specimens and any number of assays with replicates, missing data, and arbitrary per-assay naming conventions, but still have harmo ...
written 10 weeks ago by Levi Waldron380
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Answer: A: Reproducibility of MultiDataSet Comparison
... I can't comment on MultiDataSet, but I can say that MultiAssayExperiment was designed by a large number of contributors over more than two years. It was really challenging to design something that would be extensible to an open-ended set of contained data classes (including on-disk and remote data r ...
written 10 weeks ago by Levi Waldron380
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Comment: C: Error creating DESeqDataSet from "airway" SummarizedExperiment
... Thanks Martin, that did the trick (installing from source): > biocLite("DESeq2", type="source") ...
written 5 months ago by Levi Waldron380
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Comment: A: Error creating DESeqDataSet from "airway" SummarizedExperiment
... BTW, updateObject(airway) does something, but doesn't actually let me create a DESeqDataSet: > is(rowRanges(updateObject(airway))) [1] "GRangesList" [2] "CompressedList" [3] "GenomicRangesList" [4] "GenomicRanges_OR_GRangesList" [5] "List" ...
written 5 months ago by Levi Waldron380
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Error creating DESeqDataSet from "airway" SummarizedExperiment
... Trying to run the "airway" RNA-seq workflow, I get an error when creating the the DESeqDataSet, on both release and devel (example from release below). It seems to be related to the renaming of GenomicRangesORGRangesList to GenomicRanges_OR_GRangesList: > suppressPackageStartupMessages(library( ...
genomicranges deseq2 written 5 months ago by Levi Waldron380 • updated 4 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Ovarian, CRC, and bladder were quite a bit of work, and I haven't had the resources or cancer-specific projects to do it for liver or HCC. If someone can bring time and/or money to expanding the curation approach to other cancers, I'm open to providing guidance.  ...
written 6 months ago by Levi Waldron380
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Just use the values or 2^values-1 from curatedCRCData :D. They are, by the way, very highly correlated to the TCGA microarray measurements also in the package, so I am pretty confident in them. ...
written 10 months ago by Levi Waldron380
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Oh and I missed 3) - the TCGA annotation map came directly from the level 3 data, in the script download_TCGA-RNASeqV2.sh. We only used BLAST for some old platforms without a recent annotation file available. ...
written 10 months ago by Levi Waldron380
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... 1) I believe so :D. If you want to be absolutely sure, download the level-III data for one of the samples, and check that this transformation recapitulates the original values. Although, what is currently available in the GDC may have been processed on a more recent genome so it may not be exact. 2 ...
written 10 months ago by Levi Waldron380
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... The minimum value in the original files is zero, so you can recover the original values with 2^exprs(TCGA.RNASeqV2_eset) - 1. In hindsight, I would have left these values as they were! Here is a DESCRIPTION.txt file that comes with the original files from the GDC legacy archive, describing the analy ...
written 10 months ago by Levi Waldron380

Latest awards to Levi Waldron

Popular Question 19 months ago, created a question with more than 1,000 views. For multiple ColSideColors-type annotations on a heatmap
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
Scholar 3.0 years ago, created an answer that has been accepted. For A: Gene set enrichment analysis
Autobiographer 3.0 years ago, has more than 80 characters in the information field of the user's profile.

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