User: Jonathan Cairns

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Posts by Jonathan Cairns

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Comment: C: Rcade analysis without ChIP-seq replicates
... Hi André, Apologies for the delay responding. I'm not sure why genes with M.ChIP < 0 are not being filtered out; I'll take a look when I get a chance and then get back to you. In any event, these are probably not true TF targets, so I would remove them if I were you. Jonathan ________________ ...
written 3.8 years ago by Jonathan Cairns60
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Answer: A: Rcade analysis without ChIP-seq replicates
... Hi André, First of all, I note that you are using an old version of R, which means you are using an old version of Rcade (1.0.0 not 1.4.0) - I recommend you update to the latest versions. Lack of replicates is indeed going to decrease the posterior probabilities. This is because without replicate ...
written 3.8 years ago by Jonathan Cairns60
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European Developers' Meeting 2013
... Dear Bioconductor developers, We are delighted to announce this year's European Developers' Meeting, which will take place at the Centre for Mathematical Sciences in Cambridge, UK, on December 9-10, 2013. The meeting is aimed at bioinformaticians, programmers and software engineers who contribute ...
written 4.1 years ago by Jonathan Cairns60
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Comment: C: do we need remove PCR duplicate before we look for DE genes
... Hi Lucia, I'm not Simon, but my preferred strategy regarding duplicate removal for TF ChIP-seq is to remove duplicates when peak-calling, but not when doing read-based analysis (i.e. using a differential count algorithm on small, defined genomic bins) for similar reasons to the ones Simon described ...
written 4.5 years ago by Jonathan Cairns60
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Exon Arrays - GC & how many pm features?
... Hi all, I'm a little confused by Exon Array analysis in oligo. Specifically, I've been wondering if I should be correcting for GC content. The plots I get from following the vignette indicate that there is significant GC bias in my data, but the vignette doesn't appear to perform a GC correction la ...
oligo written 4.7 years ago by Jonathan Cairns60
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Comment: C: plotting BED intervals to TSS regions
... Hi, For what it's worth, I would also suggest having a look at the package ChIPpeakAnno, since it is designed to map peaks to genes. (I use its functionality to plot histograms of the positions of 5'/3' ends of peaks, relative to TSSs.) However, as far as I know, ChIPpeakAnno cannot do coverage-sty ...
written 4.8 years ago by Jonathan Cairns60

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