User: ew152

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ew1520
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Posts by ew152

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Comment: C: How to judge DESeq2_block and EdgeR_block result
... Hey Rory, Thank you so much for your help! I made three MA plots according to your suggestion. I think it is a little bit tricky to tell if the non-normalized plot is above/below the zero line. Do you mind taking a look of the three graphs? I can email those to you. Best, Ergang ...
written 9 weeks ago by ew1520
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How to judge DESeq2_block and EdgeR_block result
... Hi, I am using the Diffbind package to do the differential binding analysis for my ATAC-seq library. I followed the instruction to use blocking methods for my library, because I assumed there were substantial batch effects. Since I didn't know which one of DESeq2_block and Edger_block would generat ...
edger diffbind deseq2 differential binding analysis written 9 weeks ago by ew1520 • updated 9 weeks ago by Rory Stark2.3k
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ChIPQC 0 unmapped does not agree with the samtool generated stats
... Hi, I apologize if I missed this question somewhere. I am new to the ChIPQC package. When I put my bam file into the ChIPQC, it always gives me unmapped read =0. I know this is not the case as the bam file is simply generated by samtools sort. If I feed this bam file to samtools idxstats, it will ...
chipqc written 9 weeks ago by ew1520
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Comment: C: Error When using dba.count() in DiffBind
... Thank you so much! ...
written 3 months ago by ew1520
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Comment: C: Error When using dba.count() in DiffBind
... I think dba.count is not working on R 3.4.2, since https://support.bioconductor.org/p/102750/ this person also posted this problem after they updated their R version (although he said its 3.4.1, but it is posted 7 days ago so I assume he meant 3.4.2). Your help to fix this issue is greatly appreciat ...
written 3 months ago by ew1520
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Comment: C: Error When using dba.count() in DiffBind
... Hi Gord, Adding bUseSummarizeOverlaps = TRUE does seems to solve the issue. However, I am just wondering if this would alter the output file or not? Thank you! ...
written 3 months ago by ew1520
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Comment: C: Error When using dba.count() in DiffBind
... Sorry I am new to R. I reinstalled it, and it still gave me the same error. Does it have anything to do with the Mac Clang? Would change my version of R solve this problem? ...
written 3 months ago by ew1520
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Error When using dba.count() in DiffBind
... Hi, I was trying to use DiffBind to analyze my ATAC-Seq data. When I call the dba.count() function, I got the following error message: Error: Error processing one or more read files. Check warnings(). In addition: Warning messages: 1: In mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.r ...
diffbind dba.count atac-seq written 3 months ago by ew1520 • updated 3 months ago by Gord Brown560

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