User: Sunny Yu Liu

gravatar for Sunny Yu Liu
Sunny Yu Liu80
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5 years, 7 months ago
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5 years, 11 months ago
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s****@lunenfeld.ca

Posts by Sunny Yu Liu

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Up & Downregulated genes using DESeq
... Clear enough! Thanks a lot! -----Original Message----- From: Simon Anders [mailto:anders@embl.de] Sent: Tue 3/27/2012 4:05 PM To: Sunny Yu Liu Cc: bioconductor@r-project.org Subject: Re: [BioC] Up & Downregulated genes using DESeq HU Sunny On 2012-03-27 21:24, Sunny Yu Liu wrote: > Great ...
written 5.7 years ago by Sunny Yu Liu80
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Answer: A: Up & Downregulated genes using DESeq
... Great explanation! Thanks! Have to clarify that when I mention foldchange 2, it is not log2. For differentiated expression genes, if taking high confident hits for downstream validation and analysis, it should be more consistent and reliable. However, I think false positive rate should increase for ...
written 5.7 years ago by Sunny Yu Liu80
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Answer: A: Up & Downregulated genes using DESeq
... Because no matter how fancy the statistics is, we have to find something having biological significance. For example, in most time, even have p<0.000000000001, still get no biological effects. For most gene expression change, people always use fold change 2 as a cutoff for microarray or qPCR. As ...
written 5.7 years ago by Sunny Yu Liu80
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Answer: A: creating GRanges and reading BAM files
... Cool, and how to transfer GRanges or GRanges list to Bed format. Thanks! -----Original Message----- From: bioconductor-bounces@r-project.org on behalf of Michael Lawrence Sent: Wed 3/7/2012 10:21 AM To: David A. Cc: Bioconductor Subject: Re: [BioC] creating GRanges and reading BAM files On Wed, M ...
written 5.7 years ago by Sunny Yu Liu80
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SNP calling pipeline help
... Dear all, I am working on call SNPs and genotyping from RNAseq data. There is a lot of information online based on samtools pileup information and I am kind of lost, so is there any summary of a pipeline for this purpose? Thanks a lot for any of your helps! Yu [[alternative HTML version ...
rnaseq written 5.7 years ago by Sunny Yu Liu80
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Answer: A: how to set R memory limit
... For Windows, try memory.limit( size=XXX) check memory limit: memory.size(max=TRUE) For Mac or Linux, may try mem.limits(nsize=NA, vsize=NA) to check or set memory size maybe this is helpful for the question here -----Original Message----- From: bioconductor-bounces@r-project. ...
written 5.9 years ago by Sunny Yu Liu80
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Answer: A: Using GTF gene annotation to build a GemomicRanges Object
... worthy to have a try... thanks! -----Original Message----- From: Michael Lawrence [mailto:lawrence.michael@gene.com] Sent: Tue 11/29/2011 6:08 PM To: Sunny Yu Liu Cc: Vincent Carey; bioconductor@r-project.org Subject: Re: [BioC] Using GTF gene annotation to build a GemomicRanges Object The rtrack ...
written 6.0 years ago by Sunny Yu Liu80
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Answer: A: Using GTF gene annotation to build a GemomicRanges Object
... Thanks! I also have an idea to do it.... wish it works... -----Original Message----- From: Vincent Carey [mailto:stvjc@channing.harvard.edu] Sent: Tue 11/29/2011 3:49 PM To: sunny [guest] Cc: bioconductor@r-project.org; Sunny Yu Liu Subject: Re: [BioC] Using GTF gene annotation to build a Gemomic ...
written 6.0 years ago by Sunny Yu Liu80

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