User: sheng zhao

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sheng zhao90
Reputation:
90
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New User
Location:
Germany
Last seen:
4 years, 2 months ago
Joined:
7 years, 2 months ago
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h**********@gmail.com

Posts by sheng zhao

<prev • 9 results • page 1 of 1 • next >
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Comment: C: DEseq for chip-seq data normalisation
... Hi, I always think I should use IDR from ENCODE to get some peaks from replicates, then move to Diffbind/DESeq. How do you think? PS: IDR: https://sites.google.com/site/anshulkundaje/projects/idr Regards, Sheng On Wed, Nov 6, 2013 at 10:18 AM, Davide Cittaro wrote: > Dear Lucia, > > ...
written 5.8 years ago by sheng zhao90
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Question about quality of biological replicates from RNAseq data
... Dear all, I am using edgeR to analyse one of my RNAseq data. In this experiment, we have three tumour samples from three different patients. Named: Patient_1, Patient_2, Patient_3 We did RNASeq on Tumour-cells under two different conditions: treated and untreated, and wanted to find differenti ...
rnaseq edger written 6.1 years ago by sheng zhao90
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Question about quality of biological replicates when using edgeR
... Hi Mark and others , I am using edgeR to analyse one of my RNAseq data. In this experiment, we have three tumour samples from three different patients. Named: Patient_1, Patient_2, Patient_3 We did RNASeq on Tumour-cells under two different conditions: treated and untreated, and wanted to find d ...
rnaseq edger written 6.1 years ago by sheng zhao90
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Comment: C: edgeR/DESeq for ChIP-seq analysis
... Hi, I want to continue this discussion. I saw in some papers, people used edgeR and DESeq to analysis differentially bound between different sample groups following ChIP- seq. But most of them are studying transcription factors. Is it the case for histone modifications ChIP-seq (H3K4me1, H3K4me2 ...
written 6.8 years ago by sheng zhao90
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DEXSeq: Error: all(unlist(lapply(design, class)) == "factor") is not TRUE
... Hi, I run the example of read.HTSeqCounts() from DEXSeq, get following Error: Error: all(unlist(lapply(design, class)) == "factor") is not TRUE Any suggestion? Thanks in advance. Regards, Sheng code: library(DEXSeq) inDir = system.file("extdata", package="pasilla", mustWork=TRUE) annotationf ...
dexseq written 7.0 years ago by sheng zhao90 • updated 7.0 years ago by Alejandro Reyes1.7k
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Comment: C: [ChIPpeakAnno] Can not start ChIPpeakAnno after update to version 2.5.9
... Hi Dan, Martin and others, Thanks. Following your guide, this problem is fixed. It is should be a notice to people working on mac and using devel Bioconductor :) Regards, Sheng > I experienced the same problem, but fixed it by following Prof. > Ripley's advice and updating to R-patched ( ...
written 7.2 years ago by sheng zhao90
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Comment: C: [ChIPpeakAnno] Can not start ChIPpeakAnno after update to version 2.5.9
... Hi Martin, thank you for your help. Follow your guide : ------ source('http://bioconductor.org/biocLite.R') biocLite(character()) ------ I updated all old packages. I also checked the version of GO.db > packageDescription("GO.db")$Version [1] "2.7.1" But I am very sorry to say that I stil ...
written 7.2 years ago by sheng zhao90
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Comment: C: [ChIPpeakAnno] Can not start ChIPpeakAnno after update to version 2.5.9
... Hi Steve, thank you for your help. But I still face this problem even after I reinstalled R (version 2.15.0) and reinstalled all packages I need to devel versions . With other packages I am using, for example: cummerbund 1.99.2, under devel version , everything is working fine. I tested also al ...
written 7.2 years ago by sheng zhao90
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[ChIPpeakAnno] Can not start ChIPpeakAnno after update to version 2.5.9
... Dear all, I updated ChIPpeakAnno to 2.5.9 by: useDevel(TRUE) source("http://www.bioconductor.org/biocLite.R") biocLite("ChIPpeakAnno") After that, I got the following wrong Error information when starting ChIPpeakAnno: Loading required package: DBI Error : .onLoad failed in loadNamespace() for ...
chippeakanno written 7.2 years ago by sheng zhao90 • updated 7.2 years ago by Steve Lianoglou12k

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