User: rached

gravatar for rached
rached40
Reputation:
40
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New User
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Last seen:
8 months ago
Joined:
1 year, 9 months ago
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r********@gmail.com

Posts by rached

<prev • 5 results • page 1 of 1 • next >
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Comment: C: GRanges - changing seqlevels
... This seems to simply append a "chr" prefix to all seqlevels. This can be a problem for mitochondrial DNA, which Ensembl refers to as MT whereas UCSC refers to as chrM. Edit: apologies, I was wrong about this. MT DNA name is handled appropriately. ...
written 8 months ago by rached40
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Comment: C: Pre-processing RNA-seq data (normalization and transformation) for GSVA
... Thank you for the clarification! ...
written 17 months ago by rached40
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Pre-processing RNA-seq data (normalization and transformation) for GSVA
... I'm looking for guidance on RNA-seq data pre-processing for GSVA. The GSVA package implements several methods for computing sample-wise gene set enrichments scores: GSVA, ssGSEA, z-score and PLAGE From reading about these methods, it's apparent to me that GSVA, z-score, and PLAGE require library ...
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Comment: C: Error thrown by GSEABase::getBroadSets function: Error: 'getBroadSets' failed to
... getBroadSets successfully ran after I updated R and GSEABase to match the versions you mentioned. Thank you! ...
written 21 months ago by rached40
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Error thrown by GSEABase::getBroadSets function: Error: 'getBroadSets' failed to create gene sets: invalid BroadCollection category: 'archived'
... I receive an error when I attempt to load the latest version of the MSigDB xml file (version 6.1): > MSigDB <- getBroadSets('msigdb_v6.1.xml'); Error: 'getBroadSets' failed to create gene sets: invalid BroadCollection category: 'archived' Is anyone aware of a possible solution? > se ...
gseabase getbroadsets invalid broadcollection category archived msigdb v6.1 written 21 months ago by rached40 • updated 21 months ago by Robert Castelo2.3k

Latest awards to rached

Student 17 months ago, asked a question with at least 3 up-votes. For Pre-processing RNA-seq data (normalization and transformation) for GSVA

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