User: Wolfgang RAFFELSBERGER

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Posts by Wolfgang RAFFELSBERGER

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Answer: A: RE : RE : rsamtools installation
... Thank you Martin for taking your time to look into the problems indicated. Based on your help I was able to resolve both problems !!! In fact, an outdated version of zlib (as suspected not the copy in /usr/include/zlib.h ) was the problem for both errors I had reported (Rsamtools and RSQLite). So Ma ...
written 7.4 years ago by Wolfgang RAFFELSBERGER130
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Comment: C: rsamtools installation
... Dear List, I have trouble too installing Rsamtools and RSQlite with R-2.14.0 on a RedHat system (installation of previous R & BioC versions had no problems on the same system). In the case of RSQlite I'll try if there is a way of updating/grading our C compiler, but for Rsamtools I don't know wh ...
written 7.4 years ago by Wolfgang RAFFELSBERGER130
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using BioMart to query UniProt identifiers
... Dear list, Context : I'd like to calculate GO enrichments for a list of UniProt identifiers (note that they are "ID" or "Entry name" and NOT "AC" or "Accession"). So I tried to use BioMart to extract the GO-IDs for my list of UniProt identifiers, see code below. Basically after calling getBM() R do ...
go biomart written 8.1 years ago by Wolfgang RAFFELSBERGER130 • updated 8.1 years ago by Steffen Durinck540
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Comment: C: designing an eSet derived object
... Dear Martin, thank's again - I've got things working as you explained. Just to make sure I completely understood: Now everything is streamlined for the storage of the multiple ExperssionSets for the various methods employed (the 1st slot in my GxSet). The next step is then to review how I'm storin ...
written 8.4 years ago by Wolfgang RAFFELSBERGER130
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Comment: C: designing an eSet derived object
... Dear Martin, thank you very much for your helpful input. I'm sorry I have to bug you again. I was about there, but at the recent Bioconductor Developer Meeting I got another intersting suggestion, which I haven't succeded implementing. Briefly, (if I understood right) the idea was rather to make a ...
written 8.4 years ago by Wolfgang RAFFELSBERGER130
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Answer: A: core bioconductor packages
... follow the instructions on : http://www.bioconductor.org/install/index.html HTH, Wolfgang ________________________________________ De : bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] de la part de Pradeep Battula [prabat at utu.fi] Date d'envoi : vendredi 5 no ...
written 8.5 years ago by Wolfgang RAFFELSBERGER130
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designing an eSet derived object
... Dear list, basically I'm trying to design an object to contain the following microarray-data 1) "gxIndData": microarray-data normalized in parallel by (an array- dependent) number of n methods plus the corresponding expression-calls (again, <= n methods), 2) "gxAvData": derived values (replica ...
annotation written 8.5 years ago by Wolfgang RAFFELSBERGER130 • updated 8.5 years ago by Martin Morgan ♦♦ 23k
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problem installing package GLAD under R-2.10.0
... Dear list, all at sudden I have problems installing and/or loading the package "GLAD". The installation part seems to work OK well on Windows XP but Linux tells me already at this level about a problem at the configuration level. Anyway, neither on Windows XP as in Fedora Linux can't load it after ...
written 9.4 years ago by Wolfgang RAFFELSBERGER130 • updated 9.4 years ago by Philippe Hupé20
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testing triangular setup for finding instances of "all are different"
... Dear List, I'm trying to find out the best procedure to treat the following "triangular" experimental plan. Three groups of samples (prepared as triplicates and run on 3+3+3=9 microarrays) are to be compared in the way where those elements/genes that are different in each of the three groups should ...
limma written 9.5 years ago by Wolfgang RAFFELSBERGER130 • updated 9.5 years ago by James W. MacDonald49k
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multiple Affy normalization results in single object ?
... Dear list, I'm wondering if / how I could store the results from multiple multiple Affy summarization/normalization approaches (eg RMA, vsn, etc) in a single object. Does the Biobase ExpressionSet support this ( I haven't succeded in doing so) or do I have to create a now class of objects ? Of cou ...
biobase vsn written 9.6 years ago by Wolfgang RAFFELSBERGER130 • updated 9.6 years ago by Martin Morgan ♦♦ 23k

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