User: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe90
Reputation:
90
Status:
Trusted
Location:
Guy's Hospital, London
Website:
https://github.com/kev...
Twitter:
KevinBlighe
Scholar ID:
Google Scholar Page
Last seen:
6 days, 10 hours ago
Joined:
10 months, 2 weeks ago
Email:
k****@clinicalbioinformatics.co.uk

*also Moderator on Biostars: biostar41557

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Developer / Maintainer of Bioconductor packages:

Posts by Kevin Blighe

<prev • 47 results • page 1 of 5 • next >
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Comment: C: TCGA MAF (Mutations) data
... From where did you obtain the MAF file? - please be very specific. The TCGA samples were processed at different institutes / centres, and each would have produced a separate MAF file. If a patient's mutation data is not in one MAF file, it may be in another that you need to download. ...
written 12 days ago by Kevin Blighe90
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Comment: C: adapter trimming paired vs unpaired reads
... Ciao Maria, Trimmomatic is not a Bioconductor package, and is not written in R Programming Language. This support forum is primarily for Bioconductor packages. The paired output from Trimmomatic is what you should use for alignment. For more details, I suggest posting on Biostars, which is for more ...
written 19 days ago by Kevin Blighe90
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Comment: C: edgeR: Strange volcano plot
... Generally one plots the negative log10 of the nominal p-value ...
written 20 days ago by Kevin Blighe90
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Comment: C: Heatmap of subset of genes from data matrix file
... Did you, literally, copy and paste this from an assignment that you have been given? ...
written 20 days ago by Kevin Blighe90
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Comment: C: ComBat normalization for batch effect change 0 values
... This is why ComBat should never be used with RNA-seq. I am not sure why you chose to use it in the first place. I used it once, looked away in horror, and then never touched it again. ...
written 23 days ago by Kevin Blighe90
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Comment: C: GEOquery: HTTP error 403
... I just came to post about this, too. It is causing some Bioconductor packages to fail to build. Also reported on Biostars: https://www.biostars.org/p/377082/#377212 ...
written 24 days ago by Kevin Blighe90
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Answer: A: New to bioinformatics
... As you added a `limma` tag, too, I thought to post a link to this presentation by Gordon Smyth: Differential Expression Analysis using limma (originally found by Friederike). You should also be aware of the Biostars community (where I am Moderator): https://www.biostars.org/ Whereas Bioconductor i ...
written 28 days ago by Kevin Blighe90
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Comment: C: biomaRt returns all NAs for hgnc_symbol
... ...and it should not be any value other than NA because HGNC is for human gene nomenclature. ...
written 29 days ago by Kevin Blighe90
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Comment: C: How do I creat an expressionset if there is no GDS listed on the GEO database?
... Cross-posted on Biostars: https://www.biostars.org/p/375683/ ...
written 5 weeks ago by Kevin Blighe90
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Comment: C: RPM data analysis with DESeq2
... Cross-posted on Biostars: https://www.biostars.org/p/375275/ ...
written 5 weeks ago by Kevin Blighe90

Latest awards to Kevin Blighe

Supporter 4 months ago, voted at least 25 times.
Autobiographer 10 months ago, has more than 80 characters in the information field of the user's profile.

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