User: Jon Manning

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Jon Manning90
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Posts by Jon Manning

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Diffbind: blocking factors in a contrast not including all samples (bug?)
... Hi all, I have a fairly complex ChIP-seq experiment with lots of treated/untreated groups, 2 replicates each. All the 'replicate 1s' were generated together, separately to the 'replicate 2s' and I can see that that effect is quite pronounced in the final matrices, to the extent that it's stronger t ...
diffbind batch effect written 15 months ago by Jon Manning90
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Comment: C: Running featureCounts() in 'IntersectionStrict' mode
... Thank you for the response. With this feature, and possibly the ability to use GenomicRanges objects rather than make SAF data frames, I'd never need to use the summarizeOverlaps. ...
written 17 months ago by Jon Manning90
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Running featureCounts() in 'IntersectionStrict' mode
... Hi all, I'm counting reads to features, using featureCounts() via Rsubread, which is very nice, and fast- thank you. For a particular application I need my variable-length, single-ended reads to fall entirely within the features, as in the IntersectionStrict mode of summarizeOverlaps() et al. Is t ...
rsubread featurecounts summarizeoverlaps written 17 months ago by Jon Manning90
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Comment: C: Bug in GSVA with methods other than default?
... Hi Robert, I confirm the fix worked (though I don't think the new version is in the repo yet so I installed from source). Could there maybe be some more documentation in the gsva() help page on bootstrapping and how it doesn't apply to the other methods? Thanks, Jon On 21/02/2014 15:08, Robert ...
written 3.7 years ago by Jon Manning90
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Comment: C: Bug in GSVA with methods other than default?
... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ...
written 3.8 years ago by Jon Manning90
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Comment: C: Bug in GSVA with methods other than default?
... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ...
written 3.8 years ago by Jon Manning90
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Answer: A: Bug in GSVA with methods other than default?
... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ...
written 3.8 years ago by Jon Manning90
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Bug in GSVA with methods other than default?
... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ...
written 3.8 years ago by Jon Manning90
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Control probe QC plots for Infinium 450k chips (lumi, minfi...)
... Hi Bioconductors, I'm trying to find out if there are good existing ways in Bioconductor of plotting out the QC data from Illumina Methylation 450k chips. I want to plot the control probe intensities separately for green and red channels, label the individual probe types properly (such as 'DNP (Hig ...
annotation probe lumi minfi written 4.2 years ago by Jon Manning90 • updated 4.2 years ago by Tim Triche4.2k
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Paired RankProducts analysis
... Hello Bioconductors, I'd like to use Rank Products to analyse some proteomic data on paired samples. What would be the best way to incorporate pairing information into the call(s) to RankProd? Many thanks, Jon -- The University of Edinburgh is a charitable body, registered in Scotland, with reg ...
written 4.3 years ago by Jon Manning90

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