User: Wolfgang Raffelsberger

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Posts by Wolfgang Raffelsberger

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Answer: A: snapCGH fails in runBioHMM
... Hi Ramon, just to say that I posted another message concerning an error with snapCGH package on this list on may 4th, but got no reply. I my case it was one particular array that for some reason caused runBioHMM() to stall. I found a workaround, by just inverting R & G channel for the array ca ...
written 10.5 years ago by Wolfgang Raffelsberger160
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error in runBioHMM() (package snapCGH)
... Dear list, when analyzing Agilent 44k (human) CGH data* *using the function runBioHMM() from the library snapCGH I've run into an error message described below. Curiously this error has never occurred before although I've been using more or less the same code with previous data-sets where the code ...
cgh snapcgh written 10.6 years ago by Wolfgang Raffelsberger160
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Answer: A: error with ontoCompare (goTools)
... Just as additional information : I found out that this problem might to be specific to Windows (with R-2.8.0). I managed to run the same code on Linux with R-2.8.0 without the error message ... Wolfgang > sessionInfo() R version 2.8.0 (2008-10-20) x86_64-unknown-linux-gnu locale: C attached ...
written 10.8 years ago by Wolfgang Raffelsberger160
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error with ontoCompare (goTools)
... Dear list, I'm interested in making a graph (pie-chart or similar) showing the different GO ontologies one may get from a list of genes (in my case a list of Affymetrix probe-sets). In this context it might be good only to compare a given level of GO-ontologies (to avoid redundancies with terms clo ...
go hgu133a graph gotools written 10.8 years ago by Wolfgang Raffelsberger160 • updated 10.8 years ago by Alex Sanchez90
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exonmap error & questions (Affy mouse exon arrays)
... Dear Bioconductors, I have a few questions concerning the use of the exonmap package for (mouse) Affymetrix exon arrays : Following the instructions from the exonmap-vignette or the "example workflow" one typically first creates a vector called 'sigs' containing the retained/selected (row)names of ...
exonmap written 11.4 years ago by Wolfgang Raffelsberger160
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Limma design question (model interactions)
... Dear list, here a question about the appropriate design of a specific test layout for use with limma. The problem seems almost trivial, but among the numerous postings I haven?t found something resolving my problem : I have 2 samples (A and B) that were hybridized against a (common) reference (Ref) ...
limma written 11.5 years ago by Wolfgang Raffelsberger160 • updated 11.5 years ago by Naomi Altman6.0k
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How to read a data.frame into limma or marray
... Dear list, the question might seem trivial, I just couldn't find a function to transform a simple data.frame with microarray log2-ratios into a limma-type ot marray-type objects. I have a data.frame containing (R/G-) log2-ratios for the each slide in a separate column and I 'd like to use some of t ...
microarray normalization limma marray written 12.0 years ago by Wolfgang Raffelsberger160 • updated 12.0 years ago by Saroj Mohapatra450
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Answer: A: which package to cluster microarray data?
... Hi Alessandro, besides hclust you may also look at the package pvclust (www.is.titech.ac.jp/~shimo/prog/pvclust/ and cran.r-project.org/doc/packages/pvclust.pdf). Just note that the bootstrap calculations take a lot of time ! Wolfgang Alessandro Fazio a ?crit : > Hello! > > I would lik ...
written 12.2 years ago by Wolfgang Raffelsberger160
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problem with function to interrogate x:Map (exonmap)
... Dear list, following the instructions in the help-pages (exonmap.pdf) I get to a list of 'significant' exons/genes (sigs) but when interrogating xMap (which we have installed locally with the most recent version of mySQL) the query-functions always return empty vectors. After looking more carefull ...
survival genefilter affy plier affyio exonmap written 12.2 years ago by Wolfgang Raffelsberger160
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Comment: C: getGEO function to load files from other locations than GEO ?
... Hi Sean, as you suggested her the output from readLines() : > readLines('GSM180487.txt',n=10) [1] "TYPE\ttext\ttext\ttext\ttext\tinteger\tfloat\tfloat\ttext\ttext\ttext \tinteger\ [2] "FEPARAMS\tProtocol_Name\tProtocol_date\tScan_Date\tScan_ScannerName\t Scan_NumCh [3] "DATA\t44k_CGH_0605 (E ...
written 12.5 years ago by Wolfgang Raffelsberger160

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