## User: Kevin Blighe

Kevin Blighe340
Reputation:
340
Status:
Trusted
Location:
Website:
https://github.com/kev...
@biostar41557
Scholar ID:
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:

#### Posts by Kevin Blighe

<prev • 104 results • page 1 of 11 • next >
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... 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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65
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... 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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... 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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34
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... 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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64
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written 9 days ago by Kevin Blighe340
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48
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... Cross-posted: https://www.biostars.org/p/406248/ ...
written 12 days ago by Kevin Blighe340
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... 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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77
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... 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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... 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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65
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... 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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