## User: Kevin Blighe

Kevin Blighe170
Reputation:
170
Status:
Trusted
Location:
Website:
https://github.com/kev...
CelticBiostar
Scholar ID:
Last seen:
11 hours ago
Joined:
1 year 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 • 61 results • page 1 of 7 • next >
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... Typically, we filter the raw counts, then normalise, and then make statistical inferences on the normalised counts. After that, we may apply a further transformation on the normalised counts for the purposes of conducting downstream analyses. ...
written 2 days ago by Kevin Blighe170
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... I see. Gordon has already answered. Based on your logic, you have CPM counts, and then you apply TMM to those? ...
written 2 days ago by Kevin Blighe170
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... You should take a look at point 4 in the WGCNA FAQ: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/faq.html ...
written 3 days ago by Kevin Blighe170
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... *biomaRt* is supreme for annotation. If you have issues with your connection, then you could obtain an entire table via *biomaRt* on a once off basis, and then save and date-stamp it. You can then re-use that for annotating. This may actually be better because then you have version control in place. ...
written 12 days ago by Kevin Blighe170
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... Type ?results and read through the manual entry that appears. Then, you will understand better the output of the resultsNames command. There is also more information, here, in the vignette: Contrasts. ...
written 13 days ago by Kevin Blighe170
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... Thanks - now I see it. Why is the first column of your count matrix the gene names? - they should be rownames. I do not immediately see anything else that is unusual. This is probably something that we could fix quickly if we were at your computer, but difficult while remote. If I may suggest that y ...
written 13 days ago by Kevin Blighe170
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... That figure is not showing your colData (?) - there is only a single column of gene names? ...
written 14 days ago by Kevin Blighe170
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... Cross-posted on Biostars: https://www.biostars.org/p/387570/ ...
written 14 days ago by Kevin Blighe170
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... What have you tried so far, and where, exactly, does the uncertainty lie? Generally, people like to see that you have invested some effort before posting a question in an online forum like this. That's because we invest effort in providing answers. There are countless examples across the World Wide ...
written 20 days ago by Kevin Blighe170
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... target = "core" is primarily for Gene or Exon arrays, which typically have 'GeneChip' and/or 'ST' in their name. core will instruct the algorithm to summarise the probesets to gene or exon level. The U133 A and B arrays, which is what you are using, are fundamentally designed differently, so, th ...
written 24 days ago by Kevin Blighe170

#### Latest awards to Kevin Blighe

Supporter 6 months ago, voted at least 25 times.
Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.

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