User: Roger

Roger0
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Posts by Roger

<prev • 7 results • page 1 of 1 • next >
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... Hi, I am using Salmon to quantify reads in transcripts and aggregating them with tximport. I load the resulting object into a DESeq object with DESeqDataSetFromTximport and proceed as described in the vignette. Normally I like to present normalized expression data of certain genes as CPM/FPM, whi ...
written 6 months ago by Roger0 • updated 6 months ago by Michael Love26k
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... To whom it may concern, The vignettes of ChIPpeakAnno include an image that seems to suggest that it is possible to assign peaks to regions other than the default ones, namely microRNAs and tRNAs. However, there is no explanation anywhere in this respect, so I was wondering whether it is an actual ...
written 21 months ago by Roger0 • updated 21 months ago by Ou, Jianhong1.2k
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... Hi, I have a rather large dataset (100+ samples and growing) and I would like to examine the effect of modifying the minimum number of samples where a peak must occur to be included in my DBA object. As far as I understand, one can use the argument minOverlap in dba.count to achieve that, but this ...
written 2.4 years ago by Roger0
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... Hi, After updating R to version 3.4 and Bioconductor to 3.5, ChIPQC stops working at the "Computing metrics" step. The error messages make me suspect it might be related to changes in the 'BiocParallel' package affecting the bplapply function, but that's just a guess -- what I know for sure is that ...
written 2.4 years ago by Roger0 • updated 2.4 years ago by Thomas Carroll400
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Comment: C: Error involving ChIPQCreport
... Hi Tim, As I told you via email, the issue is fixed on ChIPQC 1.10.3 and now the report is successfully generated. Thanks! However, in case anyone reading this stumbles upon the same, I would like to report an error uploading the ChIPQC experiment with R version 3.2 and Bioconductor 3.2. The error ...
written 2.6 years ago by Roger0
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... Hi Thomas, Thanks for your quickly reply and apologies for my delay - I have been away from the office for a few days. I tried your suggestion, but unfortunately it did not work. I have just sent you an RData file containing the ChIPQCexperiment object I created (sam). I hope I am not doing anythin ...
written 2.6 years ago by Roger0
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... Hi, I have only recently come across ChIPQC, but I find it incredibly useful, especially in combination with Diffbind. Unfortunately, I can only use some its functionalities at the moment, as I keep encountering an error when I run the ChIPQCreport function: sam = ChIPQC("DBsheet_SzabiChipSeq1.cs ...
written 2.7 years ago by Roger0 • updated 2.6 years ago by Thomas Carroll400

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