User: Levi Waldron

gravatar for Levi Waldron
Levi Waldron310
Reputation:
310
Status:
Trusted
Location:
CUNY School of Public Health, New York, NY
Website:
http://www.waldronlab....
Twitter:
leviwaldron1
Scholar ID:
Google Scholar Page
Last seen:
2 days, 17 hours ago
Joined:
8 years 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/vjcitn/biocMultiAssay).

Posts by Levi Waldron

<prev • 39 results • page 1 of 4 • next >
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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 10 days ago by Levi Waldron310
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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 4 months ago by Levi Waldron310
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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 4 months ago by Levi Waldron310
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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 4 months ago by Levi Waldron310
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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 4 months ago by Levi Waldron310
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Answer: A: Possible ways of performing differential gene expression and analysis of RNA-Seq
... I can offer a couple things - 1) the survival data are in pData(TCGA.RNASeqV2_eset)[, c("days_to_death", "vital_status")] not in the exprs() - apologies if the man page makes that unclear.  2) the level-III TCGA RNA-seq data are provided as-is, BUT are log2-transformed if the maximum value is grea ...
written 4 months ago by Levi Waldron310
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Comment: C: Certificate problem with ExperimentHub / AnnotationHub
... Thanks Greg, fix confirmed. ...
written 4 months ago by Levi Waldron310
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Comment: C: Certificate problem with ExperimentHub / AnnotationHub
... Same here: > curatedMetagenomicData::LomanNJ_2013_Hi.metaphlan_bugs_list.stool() snapshotDate(): 2016-12-12 see ?curatedMetagenomicData and browseVignettes('curatedMetagenomicData') for documentation loading from cache ‘/Users/lw391//.ExperimentHub/289’ ExpressionSet (storageMode: lockedEnviron ...
written 4 months ago by Levi Waldron310
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Comment: C: About the best use of frma for several GEO Series
... These should all be equivalent since fRMA is a single-sample normalization method, no? Unlike RMA, it doesn't matter what other samples are included in your normalization, each one is normalized against their large pool of arrays.  Except that your first would require a large amount of memory.  ...
written 5 months ago by Levi Waldron310
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Answer: A: Certificate problem with ExperimentHub / AnnotationHub
... Thank you Gregory, curatedMetagenomicData is working again for me! ...
written 5 months ago by Levi Waldron310

Latest awards to Levi Waldron

Popular Question 13 months ago, created a question with more than 1,000 views. For multiple ColSideColors-type annotations on a heatmap
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
Scholar 2.5 years ago, created an answer that has been accepted. For A: Gene set enrichment analysis
Autobiographer 2.5 years ago, has more than 80 characters in the information field of the user's profile.

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