User: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe170
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170
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Website:
https://github.com/kev...
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CelticBiostar
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Last seen:
11 hours ago
Joined:
1 year ago
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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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Comment: C: RNA-Seq normalization for co-expression analysis
... 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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Comment: C: RNA-Seq normalization for co-expression analysis
... 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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Comment: C: RNA-Seq normalization for co-expression analysis
... 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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Comment: C: Best alternative annotation package to BiomaRt
... *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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Answer: C: More Info on results names
... 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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Comment: C: Deseq issues - pipeline all of a sudden stopped working
... 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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Comment: C: Deseq issues - pipeline all of a sudden stopped working
... 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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Comment: C: Low pseudo-alignment rate with Kallisto
... Cross-posted on Biostars: https://www.biostars.org/p/387570/ ...
written 14 days ago by Kevin Blighe170
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Comment: C: Differential Expression of Microarray Affymetrix data.
... 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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Comment: C: rma summarization error when normalizing using oligo and brainarray cdf
... `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

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