User: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe340
Reputation:
340
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Trusted
Location:
Website:
https://github.com/kev...
Twitter:
@biostar41557
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Google Scholar Page
Last seen:
16 minutes ago
Joined:
1 year, 4 months ago
Email:
k****@clinicalbioinformatics.co.uk

*also Moderator on Biostars: biostar41557

From The Emerald Isle. I have worked in bioinformatics as postdoc and freelance consultant in Europe, USA, and South America, both in academia and private industry, and also in clinical genetics / health services.

Developer / Maintainer of Bioconductor packages:

LinkedIn: https://www.linkedin.com/in/clinicalbioinformatics/

 

Posts by Kevin Blighe

<prev • 104 results • page 1 of 11 • next >
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Answer: A: Question regarding "low counts" in DESeq2
... You should show all of your code so that we can better understand what may be happening. For example, how are you even generating these summary results?; what is your threshold for 'low counts'?; what is your design formula? Can it be that a `high` concentration 'switches off' the expression of gen ...
written 3 days ago by Kevin Blighe340
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Comment: C: How I interpret this plot from pathview
... Hey, > CXCL1 is an important gene in IL-17 signalling pathway You need to be able to determine this based on the evidence that you are generating. > CXCL1 is ... a kind end product of this pathway I am not sure how you can determine this. ...
written 3 days ago by Kevin Blighe340
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Answer: A: How I interpret this plot from pathview
... The red colour relates to precisely what you have said, i.e., the fact that *CXCL1* has heightened expression levels in your data and is up-regulated in your treated group. Conversely, green, in this case, would indicate low expression / down-regulation. However, the precise interpretation of the c ...
written 4 days ago by Kevin Blighe340
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Answer: A: A question about the results of DESeq2
... This has little to do with DESeq2, *per se*. Your next step should be to perform some type of gene enrichment. Programs that I use routinely for this purpose include: - topGO (Bioc) - KEGGprofile (Bioc) - enrichR (CRAN) There are many other gene enrichment programs out there; so, take ...
written 4 days ago by Kevin Blighe340
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Comment: C: In SVA, the percent of biological variable of interest didnot change after addin
... Please read through this thread: https://support.bioconductor.org/p/125386/ ...
written 9 days ago by Kevin Blighe340
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Comment: C: plotEigengeneNetworks WGCNA add ME labels to left side of figure
... Cross-posted: https://www.biostars.org/p/406248/ ...
written 12 days ago by Kevin Blighe340
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Answer: A: RNAseq PCA resembles subject-specific effect in a paired study design
... You are claiming that there is a problem based solely on the PCA biplots that you have generated? There is not necessarily any problem - sample-specific effects can often be greater than your biological condition of interest. You should take a look at the percent explained variation on your PCs, pr ...
written 14 days ago by Kevin Blighe340
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Comment: C: DESeq2 PC1 variance on the PCA plot does not match proportion of variance
... The information is in the manual pages. Basically, the DESeq2 PCA implementation [by default] selects the top 500 variables based on variance, and then conducts PCA on these. This number of variables is controlled by the `ntop` parameter. As the PCA transformation is fundamentally based on covarianc ...
written 16 days ago by Kevin Blighe340
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Answer: C: Diffbind for regressing multiple confounding variables (blocking factors)
... Hey Mel, there was a previous answer here: https://support.bioconductor.org/p/101212/#101422 However, it seems that the functionality is not properly implemented. You may try the suggestion to use DESeq2, or csaw. Also to link to your former question: https://support.bioconductor.org/p/125858/ ...
written 16 days ago by Kevin Blighe340
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Answer: A: Multi-group design when performing DE analysis
... In your code, you do not define the following objects (although we can infer what they are): res.two.groups res.all.groups.together By removing samples from your dataset, the size factors that are calculated will differ (please review the DESeq2 published manuscript). Your `rowSums` calcu ...
written 16 days ago by Kevin Blighe340

Latest awards to Kevin Blighe

Supporter 10 months ago, voted at least 25 times.
Autobiographer 16 months ago, has more than 80 characters in the information field of the user's profile.

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