User: Sander Tan

gravatar for Sander Tan
Sander Tan20
Reputation:
20
Status:
New User
Location:
The Hyve, Netherlands
Website:
http://www.thehyve.nl/
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
1 year, 3 months ago
Email:
s********@thehyve.nl

Posts by Sander Tan

<prev • 5 results • page 1 of 1 • next >
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Comment: C: Applying varianceStabilizingTransformation to log transformed RNA seq data from
... Perhaps it's available on https://portal.gdc.cancer.gov , that should contain all the publicly released TCGA data.  ...
written 8 weeks ago by Sander Tan20
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Comment: C: trying to reproduce heat map made via cBioportal using download data
... Hi Chris! If you post your question on https://groups.google.com/forum/#!forum/cbioportal the cBioPortal community will take a look at it! Best, Sander ...
written 9 weeks ago by Sander Tan20
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Answer: A: Applying varianceStabilizingTransformation to log transformed RNA seq data from
... Hi Ben, The data in cBioPortal OncoPrint is RSEM normalized and z-scored, and therefore not compatible with DESeq2. If I remember correctly, DESeq2 requires raw counts as input data. But z-score values can be used for clustering. This can be done cBioPortal OncoPrint by clicking the "Heatmap" butto ...
written 9 weeks ago by Sander Tan20
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Comment: C: Crash GSVA 1.24.0 with bootstrapping
... Thanks Robert for the excellent solution and advice. This also explains why I didn't experience the issue with a dataset that was based on a different kind of data. ...
written 15 months ago by Sander Tan20
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Crash GSVA 1.24.0 with bootstrapping
... Hi, I recently updated GSVA to 1.24.0 and I'm still experiencing a crash when I run GSVA with bootstrapping. This is the code I ran, including with urls to RNA-Seq test data and gene set test data. library(qusage) library(GSVA) library(ggplot2) library(reshape2) ### Input files ### Skin Cutaneo ...
gsva bug written 15 months ago by Sander Tan20 • updated 15 months ago by Robert Castelo2.2k

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