User: melnuesch

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melnuesch10
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Posts by melnuesch

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Diffbind for regressing multiple confounding variables (blocking factors)
... I was wondering how Diffbind deals with the problem of using multiple blocking factors (let's say, age, gender and postmortem delay). If there is a (small) limit of how many of those I could correct at the same time. Ideally, two or three should be possible (for example, those three I named, in sequ ...
chipseq regression diffbind deseq2 block written 18 days ago by melnuesch10
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Diffbind with multiple blocking factors
... I've got a chip-seq dataset which I would like to analyse using DiffBind. I've tried Diffbind with one blocking factor and it works fine, but I was wondering how can I do it for three factors (e.g. age, gender, post-mortem delay , when dealing with tissue samples). (E.g. sample 1 : 60 years old, fem ...
diffbind model blocking written 26 days ago by melnuesch10
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Diffbind with age as blocking factor
... I have chip-seq data which I am analysing with Diffbind. I understood the "blocking factor" functionality of it can be used to remove confounding variables. In the Diffbind manual, the confounding factors used as examples are strings (e.g. cell line names, if the cells from those samples were "resis ...
diffbind chip-seq written 5 weeks ago by melnuesch10 • updated 28 days ago by Rory Stark2.9k
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Comment: C: DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from
... Thank you very much! Yes, indeed, the people I consulted were from a bioinformatics lab but they told me they specialize in RNA-seq and haven't worked much with ChIP-seq. This is why I double-checked here, since it was possible that ChIP-seq was different and RNA-seq doesn't necessarily give you exp ...
written 5 months ago by melnuesch10
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DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
... **1) Doubt about DiffBind's MA plots in general** Hello, I am doing ChIP-seq analysis of H3K4me3 in human samples across different conditions. For that, my pipeline includes DiffBind to make volcano, MA plots , PCA and heatmaps. The DiffBind manual says that MA plots are good to see the effect of no ...
chipseq diffbind R maplot written 5 months ago by melnuesch10 • updated 5 months ago by Rory Stark2.9k
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DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
... **Some background:** I am doing the differential binding analysis of some human histone ChIP-seq samples (bowtie2 mapping to hg19, duplicate marking, MACS2 narrow peak calling, blacklisted regions filtering with bedtools intersect and Anshul Kundaje's BED file for hg19). The samples are H, Y and Z ...
diffbind written 5 months ago by melnuesch10

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