User: array chip

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array chip360
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Posts by array chip

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Comment: A: DESeq2 for survival analysis
... Michael, just to make sure, if I want to use SAMseq, I should use raw counts without any normalization/transformation (not even sequence depth adjustment), juts like with DESeq(), correct? ...
written 22 months ago by array chip360
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Comment: A: DESeq2 for survival analysis
... Thank you Michael! This is very helpful. ...
written 22 months ago by array chip360
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DESeq2 for survival analysis
... Dear all, I am new to RNA-seq analysis with bioconductor. I am wondering if I can use DESeq2 directly to perform survival analysis (e.g. Cox regression)? If not directly, do I understand correctly that we should do rlog or vst transformation on the count data before running Cox regression separatel ...
survival deseq2 rlog transformation written 23 months ago by array chip360
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Answer: A: pathway analysis by SPIA using SPIA package vs graphite package
... actually I found a error in my analysis. the 2 packages now give quite similar results (though not exactly the same). sorry for the confusion John ________________________________ To: "bioconductor@stat.math.ethz.ch" Sent: Thursday, January 16, 2014 11:34 AM Subject: [BioC] pathway analysis b ...
written 5.8 years ago by array chip360
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pathway analysis by SPIA using SPIA package vs graphite package
... Hi, I was running pathway analysis with a set of differentiated genes on KEGG pathways by SPIA. I tried both SPIA package (version 2.14.0) and graphite package (version 1.8.1). But I found the results from these 2 packages are quite different. For example, the top 3 pathways from the 2 packages are: ...
pathways spia cycle graphite written 5.8 years ago by array chip360
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package installation
... Hi, when I install the package gCMAPWeb, I got the following error message: > biocLite("gCMAPWeb") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'gCMAPWeb' Warning: unable to access index for repository http://br ...
gcmapweb written 5.8 years ago by array chip360 • updated 5.8 years ago by James W. MacDonald51k
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Comment: C: DESeq2 : NA p values reported
... Wah, thanks a lot Herve! I also encountered that linking to biomaRt by "ensembl = useMart("ensembl")"�sometimes take forever, quite frustrated. John ________________________________ From: Herv� Pag�s To: Michael Lawrence ; array chip Cc: "bioconductor@r-project.org" Sent: Monday, November 25 ...
written 5.9 years ago by array chip360
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Comment: C: DESeq2 : NA p values reported
... Thansk a lot Michael ________________________________ From: Michael Lawrence Cc: Michael Lawrence ; "bioconductor@r-project.org" Sent: Monday, November 25, 2013 2:19 PM Subject: Re: [BioC] exon genomic coordinates You could use rtracklayer to grab the CCDS track from UCSC. Might be some way ...
written 5.9 years ago by array chip360
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Comment: C: DESeq2 : NA p values reported
... Thanks Michael. How do I restrict to consensus CDS? John ________________________________ From: Michael Lawrence Cc: "bioconductor@r-project.org" Sent: Monday, November 25, 2013 1:55 PM Subject: Re: [BioC] exon genomic coordinates Well, one approach is to take the longest one. That's what ...
written 5.9 years ago by array chip360
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Comment: C: DESeq2 : NA p values reported
... Hi all, have another questions about exon genomic coordinates: library(biomaRt) ensembl = useMart("ensembl") ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) > getBM(attributes = c("external_gene_id","chromosome_name","exon_chrom_start","exon_chrom_ end","ensembl_transcript_id","rank ...
written 5.9 years ago by array chip360

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Popular Question 5.8 years ago, created a question with more than 1,000 views. For CEL files not valid?
Popular Question 5.8 years ago, created a question with more than 1,000 views. For CEL files not valid?

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