User: Pete Shepard

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Pete Shepard240
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Posts by Pete Shepard

<prev • 24 results • page 1 of 3 • next >
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plotting chromosome band names in GenomeGraphs
... Hello list Is there a way to plot chromosome band names along an ideogram using genome graphs. I realize that this can be done in quantsmooth but I prefer the ideograms generated by genomegraphs. TIA [[alternative HTML version deleted]] ...
ideogram quantsmooth genomegraphs written 8.4 years ago by Pete Shepard240
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plotting probes along a chromosome
... Hello List, I am trying to graph the position of probes ~50 nucleotides in length along a chromosome and am looking for the best way to accomplish this. So far I have tried the genomeGraphs package and can plot a chromosome and its bands just fine. Next I attempt to plot assign the data coordinates ...
graph genomegraphs assign written 8.4 years ago by Pete Shepard240 • updated 8.4 years ago by Oosting, J. PATH550
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(no subject)
... Hello List, I am trying to plot the distribution of segments ~ 50 nt in length along a chromosome/chromosomes and am looking for the best way to do this. So far [[alternative HTML version deleted]] ...
written 8.4 years ago by Pete Shepard240
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minor allele frequency of snps in hapmap database
... Hello List, I am trying to calculate the minor allele frequency for all the snps in the hapmap database. I am wondering if anyone has done this? I have noticed that there seem to be two ways to attempt this. One using the snpMatrix package and the other using the bioMaRT package. Any help is greatl ...
biomart written 8.7 years ago by Pete Shepard240 • updated 8.7 years ago by Benilton Carvalho4.3k
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SNPlocs.Hsapiens.dbSNP.20101109 won't load
... Hello All, I am getting the following error: Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘SNPlocs.Hsapiens.dbSNP.20101109’ is not available when I run: biocLite("SNPlocs.Hsapiens.dbSNP.20101109") This package is from February 24, 2011 according to the pac ...
written 8.8 years ago by Pete Shepard240 • updated 8.8 years ago by Sean Davis21k
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Comment: C: rpy save session and package downloads
... and you will of course be able to load them again next time you start a session without having to re-install them I see this now The first part of my question was that my R session is not being saved because I am not 2011/2/28 Hervé Pagès > Hi Pete, > > > On 02/28/2011 03:34 PM, rn ...
written 8.8 years ago by Pete Shepard240
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Comment: C: display subset of gene symbols in heatmap
... Hi Tim, That worked at least in getting the names in the list, although I don't understand what this grep section is doing? I just want the names in some.probes? named <- data.matrix(my.exprs[ some.probes, grep('CD34', names(my.exprs)) ]) Sadly: heatmap(named, ...
written 8.8 years ago by Pete Shepard240
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Answer: A: display subset of gene symbols in heatmap
... Hi Tim, Thanks for your response. rownames(dat.n) <- make.names(mget(rownames(dat.n), hgu133a2SYMBOL, ifnotfound=NA)) and rownames(dat.n) <- mget(rownames(dat.n), hgu133a2SYMBOL, ifnotfound=NA) seems to give me the same output. dat.plotme <- dat.n[ "NPEPL1",] using this command, I ca ...
written 8.8 years ago by Pete Shepard240
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display subset of gene symbols in heatmap
... Dear List, I am attempting to visualize some affymetrix data from the hgu133a2.db chip using heatmap. So far, what I've done is as follows dat<-ReadAffy(filenames = "GSM448823.CEL", "GSM448824.CEL","GSM448816.CEL", "GSM448817.CEL") #puts .CEL files into a data frame dat2<-rma(dat) ...
hgu133a2 probe written 8.8 years ago by Pete Shepard240
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goTools question
... Hello, I have a list of gene names and I am trying to see if the Biological Process Ontologies for this list of gene names is overrepresented compared to background. Basically just two pie graphs 1 of my genes and the other all genes BP ontologies and a list of p-values. I have been looking at the ...
probe gotools written 9.2 years ago by Pete Shepard240

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Popular Question 8.4 years ago, created a question with more than 1,000 views. For minor allele frequency of snps in hapmap database

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