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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Comment: C: how to set design for this DOE in DESeq2
... 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 3 months ago by aimin.at.work0
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Comment: C: how to set design for this DOE in DESeq2
... 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 3 months ago by aimin.at.work0
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Comment: C: how to set design for this DOE in DESeq2
... 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 3 months ago by aimin.at.work0
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Comment: C: how to set design for this DOE in DESeq2
... 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 3 months ago by aimin.at.work0
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how to set design for this DOE in DESeq2
... 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 ...
deseq2 written 3 months ago by aimin.at.work0 • updated 3 months ago by Michael Love25k
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Comment: C: Compare the DNA footprinting between different samples when using ATACseqQC
... Thank you, what does the fragmentation fit line of the signals indicates? Aimin   ...
written 14 months ago by aimin.at.work0
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Compare the DNA footprinting between different samples when using ATACseqQC
... 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 ...
atacseqqc written 15 months ago by aimin.at.work0 • updated 14 months ago by Ou, Jianhong1.1k
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Comment: C: use factorFootprints function in ATACseqQC to get DNA footprinting for certain g
... 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 15 months ago by aimin.at.work0
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Comment: C: use factorFootprints function in ATACseqQC to get DNA footprinting for certain g
... 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 15 months ago by aimin.at.work0
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Comment: C: use factorFootprints function in ATACseqQC to get DNA footprinting for certain g
... 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 15 months ago by aimin.at.work0

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