User: kyliecode

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kyliecode0
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Posts by kyliecode

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Comment: C: Diffbind: edgeR or DESeq2 ?
... Hi Rory, Thanks for your suggestion about using GreyListChIP in handling the false positive signal. I'm now trying this approach.  I've got some question about applying the greylist.   If doing the filtering before peak calling: 1) How to do the filtering? 2) Do you know if this step compatibl ...
written 24 months ago by kyliecode0
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Warning in "countReads" [Warning message: In .Seqinfo.mergexy(x, y) : The 2 combined objects have no sequence levels in common.]
... Dear developer & users, Hi, I've been trying GreyListChIP but was not succeed when using own bam file (The package installation is alright, which tested by the sample data) Here's the code: library(GreyListChIP) library(BSgenome.Mmusculus.UCSC.mm10) path <- system.file("extra", package="G ...
greylistchip written 24 months ago by kyliecode0
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DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
... Hi everone, Have you ever seen "diffbind DESeq2 analysis has not been run for this contrast" during DiffBind analysis (during: plot(K9_broad_affinity, contrast=1)) I've confirmed DiffBind is workable using the test data from the package   Please find the history of my run as follows: R version 3 ...
chipseq diffbind R written 2.0 years ago by kyliecode0 • updated 2.0 years ago by Rory Stark2.8k

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