## User: aimin.at.work

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#### Posts by aimin.at.work

<prev • 13 results • page 1 of 2 • next >
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... Thank you, if so, how can I get the the log counts after adjusting batch effects? I got the the following modelMatrix  > modelMatrix Intercept group_se_rep1_vs_pe_rep1 condition_Hinfp_A_G_point_mutant_vs_FRT19A_Control_2 FRT19A_se 1 1 ...
written 1 day ago by aimin.at.work0
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... One way is, DESeq2 treats batch:residual as residual like the following way  design= ~batch + condition + batch:residual+residual  Am I right? Thank you ...
written 1 day ago by aimin.at.work0
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... Thank you, Yes, I did this way, I am just interested in how DESeq2 calculate statistics for p-values for this design, it seems in this design, the error between batches is confounding with residual error, and I did observed strong batch effect. Aimin ...
written 1 day ago by aimin.at.work0
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... I had some typo, it should be:  > ddsFullCountTable<-DESeqDataSetFromMatrix( + countData=rawdata.tli.after.filter.by.cpm, + colData=DOE.2, + design= ~batch + condition + batch:condition) > dds <-DESeq(ddsFullCountTable) estimating size factors estimating dispersions Error in ch ...
written 5 days ago by aimin.at.work0
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... I have a data set from the following Design of Experiment(DOE) ` sample batch condition FRT19A_se se FRT19A_Control_2 Hinfp_A_G_se se Hinfp_A_G_point_mutant Hinfp_M2_11_se se ...
written 5 days ago by aimin.at.work0 • updated 1 day ago by Michael Love24k
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... Thank you, what does the fragmentation fit line of the signals indicates? Aimin   ...
written 11 months ago by aimin.at.work0
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... I am using ATACseqQC to plot DNA footprinting.  I want to compare the DNA footprinting between different samples.  Would it be possible to get  DNA footprinting graphs with same scale to make them be comparable? For example, for CTCF, I got some from 0 to 0.2, other from 0 to 0.14, from 0 to 0.25, e ...
written 11 months ago by aimin.at.work0 • updated 11 months ago by Ou, Jianhong1.1k
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... OK, thank you very much. it works now. Aimin On Thu, Jul 12, 2018 at 5:23 PM, Julie Zhu [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Julie Zhu <https: support.bioconductor.org="" u="" 3596=""/> wrote Answ ...
written 11 months ago by aimin.at.work0
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... Yes, I tried, but I got the following error: bamfile <- system.file("extdata", "GL1.bam",package="ATACseqQC") which <- GRanges(seqnames = "chr1", ranges = IRanges(seq(10000, 20000, by=1000), width = 10)) seqinfo(which) <- seqinfo(Hsapiens) which\$score <- rep(1, length(which)) factor ...
written 11 months ago by aimin.at.work0
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... Thank you, Yes, I tried, but I got same error as before. Aimin > which <- GRanges(seqnames = "chr1", ranges = IRanges(seq(10000, 20000, by=1000), width = 10)) > which GRanges object with 11 ranges and 0 metadata columns: seqnames ranges strand <rle> <ira ...
written 11 months ago by aimin.at.work0

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