User: Wu, Xiwei

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Wu, Xiwei350
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Posts by Wu, Xiwei

<prev • 35 results • page 1 of 4 • next >
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DESeq with no replicates
... Dear list, I have a smallRNA sequencing data from two samples, without replicates. I tried using DESeq to identify differentially expressed gene following the manual, and the code is as below: > library(DESeq) > conds <- c("NSC", "TSC") > head(combined_data) NSC TSC ...
sequencing mirna smallrna deseq written 8.6 years ago by Wu, Xiwei350 • updated 8.6 years ago by Wolfgang Huber13k
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rtrackalyer too slow?
... Hi, I recently started to use rtracklayer, so I am still new to it. Here I am trying to get conservation score for a number of genomic loci. The code below works, but extremely slow. I found it took several seconds to get one done, so it becomes impossible when it gets to over 1000 sites. What is m ...
rtracklayer written 9.4 years ago by Wu, Xiwei350 • updated 9.4 years ago by Michael Lawrence11k
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FindOverlaps Problem
... Vince, Michael, Thanks both of you. It is good to know that the devel version works correctly. I guess it is always a good idea to get the most recent devel version. Have a great weekend! Xiwei ________________________________ From: Michael Lawrence [mailto:lawrence.michael@gene.com] Sent: Sat ...
written 9.5 years ago by Wu, Xiwei350
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Comment: C: Distinguish Synonymous vs. Non-synonymous SNPs
... Michael, Here is one example. Please let me know if I have missed anything. Thanks. > a <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 9, 5, 6, 3, 7), sep="")) > b <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 18, 5 ...
written 9.5 years ago by Wu, Xiwei350
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Comment: C: Distinguish Synonymous vs. Non-synonymous SNPs
... Dear all, I found that the findOverlaps function does not work properly if the space levels do not match exactly between subject and query. Has anyone noticed the same problem? I am using the R-2.10.0 and IRanges-1.4.0. Is this problem being fixed in the developmental version? Thanks. Xiwei --- ...
written 9.5 years ago by Wu, Xiwei350
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Comment: C: Distinguish Synonymous vs. Non-synonymous SNPs
... Michael, Thanks a lot for your help. I will give it a try. Is it good for novel SNPs not in the dbSNP? The SNPs I got are from a sequencing project, many of them are not in dbSNP. Xiwei -----Original Message----- From: Michael Dondrup [mailto:Michael.Dondrup@uni.no] Sent: Friday, January 29, 2010 ...
written 9.5 years ago by Wu, Xiwei350
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Distinguish Synonymous vs. Non-synonymous SNPs
... Dear list, I have a list of SNPs with chromosome location, and trying to see which ones are non-synonymous. Are there any packages/functions that can distinguish synonymous and non-synonymous SNPs? I tried to search the list, but could not find anything related. Thanks in advance. Xiwei ------ ...
written 9.5 years ago by Wu, Xiwei350 • updated 9.5 years ago by Michael Dondrup550
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AffyQCReport: "I'm sorry, I do not know about chip type" (celeganscdf)
... Emmanuel Levy writes: > > Hello, > > I have an error with affyQCReport: > Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about > chip type: celeganscdf > Error in plot(qc(object)) : unable to find the argument 'x' in > selecting a method for function 'plot' ...
cdf probe genefilter affy simpleaffy affyqcreport written 12.4 years ago by Wu, Xiwei350
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Answer: A: Affymetrix Promoter tiling array
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20060830/ 8f435a59/attachment.pl ...
written 12.9 years ago by Wu, Xiwei350
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Answer: A: Affymetrix Promoter tiling array
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20060830/ e2b85c39/attachment.pl ...
written 12.9 years ago by Wu, Xiwei350

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