User: bioinf

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Posts by bioinf

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Comment: C: DESEq2 for mulitple tissues under 2 conditions
... So I can use:   dds$condition <- factor(dds$condition, levels = c("wild","mutant")) How can I keep replicate numbers also during analysis and heatmap so that I can see if there is any variation between replicates? In (iii) I want to compare between different tissue types from mutant. ...
written 19 days ago by bioinf0
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Comment: C: DESEq2 for mulitple tissues under 2 conditions
... @ https://support.bioconductor.org/u/6944/ Yes, you are right WA1 is the replicate 1 of WA. A,B,C,D,E are five different tissues, while 1, 2 and 3 indicate biological replicates. Would you please elaborate more on how I can rearrange coldata to make it better accessible for DESeqDataSetFromMatrix ...
written 20 days ago by bioinf0 • updated 19 days ago by Michael Love15k
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DESEq2 for mulitple tissues under 2 conditions
... Hi, I have paired rnaseq data from multiple samples, counted with featureCounts, now planning to use DESeq2 and trying to design it. I have gone through https://support.bioconductor.org/p/67600/.  However, I would like to confirm if my design is correct or not? Here is the sample coldata: ti ...
rnaseq deseq2 R featurecounts deseqdatasetfrommatrix written 20 days ago by bioinf0 • updated 19 days ago by Michael Love15k
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Comment: C: CoverageView error (bug?)
... Hi, Did you find any solution? ...
written 5 months ago by bioinf0
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Comment: C: TarSeqQC TargetExperiment() Error- failed to stop SOCKcluster cluster-error writ
... Its running since yesterday and got the following error now: Error in `[.data.frame`(info, , "chr") : undefined columns selected In addition: Warning messages: 1: In .local(.Object, ...) : Your bed file have duplicated features. Removing duplicated ... 2: In (function (..., deparse ...
written 5 months ago by bioinf0
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Comment: C: TarSeqQC TargetExperiment() Error- failed to stop SOCKcluster cluster-error writ
... Thanks. I ran it again with the option you mentioned, but TargetExperiment() is taking a lot of time. Do you have an idea how much time it should take to process 1GB bam and 1GB fasta for TargetExperiment()? I am trying to run it from last few days, sometimes it ran for full day too.   ...
written 5 months ago by bioinf0
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Comment: C: TarSeqQC TargetExperiment() example takes forever
... Hello Gabriela, I also ran into some issue with TargetExperiment(), here are the details https://support.bioconductor.org/p/97084/ I hope if you can help me out. Thanks! ...
written 5 months ago by bioinf0
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TarSeqQC TargetExperiment() Error- failed to stop SOCKcluster cluster-error writing to connection
... Hi, TarSeqQC seems to be a wonderful package for TS. I ran it successfully on extdata (test data) on Windows 8.1 64-bit PC as well as Rstudio server, but getting following error while running on my data on Rstudio server (bam=1.2GB, fasta file=1.4GB, bed file=25MB): library(TarSeqQC) library(Bioc ...
biocparallel R ngs tarseqqc written 5 months ago by bioinf0 • updated 5 months ago by Martin Morgan ♦♦ 20k
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Comment: C: Error: HelloRanges eval
... Yes, I checked. ...
written 5 months ago by bioinf0
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Comment: C: Error: HelloRanges eval
... While running: gr_a <- import("1.bedpe", genome = genome) Error: logical subscript contains NAs Edited bedpe file and ran single commands, now again error: cov <- unname(coverage(gr_b)[gr_a]) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘ ...
written 5 months ago by bioinf0

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