User: Chris Fenton

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Chris Fenton80
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Norway
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4 years, 9 months ago
Joined:
9 years, 7 months ago
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c*****@fagmed.uit.no

Posts by Chris Fenton

<prev • 9 results • page 1 of 1 • next >
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Missing SAM header?
... Trying to follow the following recommended procedure ""http://www.nimblegen.com/products/lit/07187009001_NG_SeqCap_TechNote_EvalEZdata.pdf" Have seen a lot of similar posts on bioconductor about sam headers, unfortunately none that sheds light on this problem.  Anyone have a clue?  Thanks, Chris  ...
sequencing written 4.8 years ago by Chris Fenton80 • updated 4.8 years ago by James W. MacDonald50k
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CGHweb and cghFLasso
... Trying to automate some of the uni's CGH experiments. Have pretty much installed CGHweb. Stuck on cghFLasso. Anyone seen this error before. >>>>>>>>>>>>>>>error<<<<<<<<<<<<<<<<<<<<<<< I ...
cgh written 7.8 years ago by Chris Fenton80 • updated 7.8 years ago by Vincent J. Carey, Jr.6.3k
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Help strange GSEA error
... > source('basicGSEA.R') 'envir' chosen: encoding = "native.enc" chosen Error: '\%' is an unrecognized escape in character string starting "Tag \%" > sessionInfo() R version 2.11.0 (2010-04-22) i386-pc-mingw32 locale: [1] LC_COLLATE=Norwegian (Bokm?l)_Norway.1252 LC_CTYPE=Norwegian (Bokm?l) ...
written 9.1 years ago by Chris Fenton80 • updated 4.0 years ago by paawanpoudel0
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Control based normalization
... I have around 50 arrays each with 4 hybridization blocks. On each array is a control block. Specifically the control is a known genome which is hybridized against the annotated probe set on the chip. The control block gives a estimate on the number of false positives/negatives and is used to asses t ...
normalization probe written 9.2 years ago by Chris Fenton80
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snapCGH genomePlot chrominfo
... function (input, array = 1, naut = 22, Y = FALSE, X = FALSE, main = NA, status, values, pch, cex, col, chrominfo = chrominfo.Mb, ylim = c(-2, 2), ylb = "Log2Ratio", chrom.to.plot = NA, xlim = c(0, NA), ...) ma2 <- processCGH(ma1) seginfo.dna <- runDNAcop ...
written 9.2 years ago by Chris Fenton80 • updated 9.2 years ago by Sean Davis21k
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Nimblegen CGH ringo to snapCGH
... Has anyone gotten nimblegen CGH data from Ringo into snapCGH. I have looked at https://stat.ethz.ch/pipermail/bioconductor/2006-October/014724.html but it seems that Nimblegen has yet again changed format. For instance I find no file remotely named ORDER_ID3051_SampleKey.txt. I do have a file samp ...
cgh snapcgh ringo written 9.2 years ago by Chris Fenton80 • updated 9.2 years ago by Joern Toedling450
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pdInfoBuilder for Niblegen 12x135k array, argument "posFile" is missing, with no default
... Pretty much copied the code from http://linusben.net/wiki/index.php/Oligo.bioconductor. Something ala, """ > library(pdInfoBuilder) > filename_ndf <- list.files('.',pattern='.ndf',full.names=T) > filename_xys <- list.files('.',pattern=".xys",full.names=T)[1] > seed <- new("Ng ...
written 9.5 years ago by Chris Fenton80 • updated 9.5 years ago by Benilton Carvalho4.3k
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R question on symbolic variables
... Is this a limitation in the R language or am I missing something fundamental (like an operator) > a <- list("hello"<-c(1,2,3), "goodbye"<-c(1,2,3)) > a$hello [1] 1 2 3 > b <- "hello" > a$b NULL So how could we do the following for example. > info <- names(a) > f ...
written 9.5 years ago by Chris Fenton80 • updated 9.5 years ago by Axel Klenk930
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LIMMA problems with gpr file (ATF indentifier ?)
... Been handed a bunch of gpr files this with a two day limit to do the analysis. The problem is that I can not get LIMMA to read the gpr files. Anyone run into this problem ? I have checked the gpr file format and this seems compliant, Yet rg <- read.maimages(files=targets$FileName[1], source='g ...
limma written 9.6 years ago by Chris Fenton80 • updated 9.6 years ago by Axel Klenk930

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Popular Question 4.8 years ago, created a question with more than 1,000 views. For Missing SAM header?

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