User: Markus Schmidberger

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Posts by Markus Schmidberger

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Munich R Course - Parallel Computing with R
... Dear R users, at November 8. & 9., 2010, there will be an R course for 'Parallel Computing with R' in Munich at the super computer center. The course is part of the Munich R Course series and gives an introduction to parallel computing with R. Especially the R packages snow, snowfall, multicore ...
written 9.0 years ago by Markus Schmidberger380
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Short survey concerning the use of software engineering in the field of High Performance Computing
... Dear Colleagues, this is a short survey (21 questions that take about 10 minutes to answer) in context of the research work for my PhD thesis and the Munich Center of Advanced Computing (Project B2). It would be very helpful, if you will take the time to answer my questions concerning the use of so ...
written 9.1 years ago by Markus Schmidberger380
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Comment: C: affyPara: background correction & normalization only?
... fixed everything in 1.7.2. Thanks for using affyPara and providing feedback. Best Markus Leo Lahti wrote: > Dear Markus, > > Thanks for a quick reply. > > > I tested affyPara 1.7.1. To get the summarization method 'none' to > work, I had to slightly modify the summary.method c ...
written 9.5 years ago by Markus Schmidberger380
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Comment: C: affyPara: background correction & normalization only?
... Leo Lahti wrote: > Dear Markus, > > Thanks for a quick reply. > > > I tested affyPara 1.7.1. To get the summarization method 'none' to > work, I had to slightly modify the summary.method check in preproPara > R code ("if ((any( express.summary.stat.methods()==summary.method) ...
written 9.5 years ago by Markus Schmidberger380
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Answer: A: affyPara: background correction & normalization only?
... Dear Leo, good point. I did some changes to preproPara(). No there is a summarization method 'none' (summary.method='none') available. There will be no summarization step and the results object eset is NULL. I submitted these changes and documentation to the svn. Version 1.7.1. should be available ...
written 9.5 years ago by Markus Schmidberger380
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automatically loading of annotation package
... Hi, is there any way for an autimatic loading of the corresponding annotation packages. I have to analyze 15 different datasets with different AffyBatches from different chip types. I want to do something like that: library(affy) library(ALL) data("ALL") l <- paste(annotation(ALL), "db", sep=". ...
written 10.0 years ago by Markus Schmidberger380 • updated 9.9 years ago by Chao-Jen Wong580
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Comment: C: Normalization of array data from GEO repository
... Hi, have a look to the AE FAQ: http://www.ebi.ac.uk/microarray/doc/help/faq.html#submitter_FAQ_genera l *How much over-lap is there between ArrayExpress and the Gene Expression Omnibus (GEO)?* We import data on a weekly basis from GEO (NCBI). As a priority all GEO experiments which are in GEO data ...
written 10.1 years ago by Markus Schmidberger380
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Answer: A: KEGGgraph package: KGML files working again
... Hi David, I can confirm your message. Since Monday morning the xml files seem to be complete. Markus Jitao David Zhang schrieb: > Hi KEGGgraph users, > > I have just received an Email from KEGG staff and thanks to their work > some KGML files which did not work days before seems t ...
written 10.3 years ago by Markus Schmidberger380
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KEGGgraph, error
... Hi, I found the KEGGgraph package in the development repository. It sounds great. But it is not working. There are no edges in the graphs! What is wrong? > library(KEGGgraph) > tmp <- tempfile() > retrieveKGML('04110', organism="hsa", destfile=tmp, method="wget", quiet=FALSE) --08:5 ...
organism hgu133a kegggraph written 10.3 years ago by Markus Schmidberger380 • updated 10.3 years ago by Jitao Zhang20
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vsn add-on normalization
... Hi, I have a question for the vsn normalization towards a reference data set. (my real data are much more) I will normalize 5 Arrays with vsn: ab_ref <- ReadAffy(filenames=celfiles[1:5]) fit_ref <- vsn2(ab_ref) After this I can add 2 Arrays with normalization towards a reference: ab_add &l ...
normalization vsn written 10.4 years ago by Markus Schmidberger380

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