User: Markus Schmidberger

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Posts by Markus Schmidberger

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network analyses on genes or probesets
... Hi all, I am using affymetrix microarray data. In the raw data I have probes. After preprocessing (background correction, normalization and summarization) I have probesets. Now I can use the annotation packages (e.g. library(hgu133a.db)) to get the assignment between probesets and genes. Are there ...
microarray annotation normalization preprocessing network written 10.5 years ago by Markus Schmidberger380 • updated 10.5 years ago by Marc Carlson7.2k
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Comment: C: sequencing workshop
... If you have a computer cluster you also can use the package "affyPara". Then you have a very fast solution for large numbers of microarrays. Best Markus Wei,Caimiao wrote: > Dear all, > > I can use justRMA to read in 200+ U133_2 .Cel files and normalize at once on a sparc-sun-solaris2.9. ...
written 10.9 years ago by Markus Schmidberger380
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Comment: C: multicore processor
... You also should have a look to Luke Tierney's website and his pnmath code (using openMP): http://www.cs.uiowa.edu/~luke/R/experimental/ And there is a new mailing list for HPC: R SIG on High-Performance computing: r-sig-hpc at r-project.org. And there is a lot of other stuff for parallelization in ...
written 10.9 years ago by Markus Schmidberger380
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Answer: A: Importing "Detailed sample annotation" from ArrayExpress DB into R
... Hi, I found a working solution: an <-read.table("E-GEOD-635.sdrf.txt", header=TRUE, sep="\t") Best Markus Markus Schmidberger schrieb: > Hello, > > I am looking for a function or package to import the "Detailed sample > annotation" file from the ArrayExpress Database. > For GEO ...
written 11.1 years ago by Markus Schmidberger380
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Importing "Detailed sample annotation" from ArrayExpress DB into R
... Hello, I am looking for a function or package to import the "Detailed sample annotation" file from the ArrayExpress Database. For GEO there is the "GEOquery" package. For ArrayExpress there is the "ArraExpress" package. But I am looking for a function to import or read the "xxxxxx.sdrf.txt" file. ...
arrayexpress written 11.1 years ago by Markus Schmidberger380
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Answer: A: Maximum number of CEL files for ReadAffy() in Affy package.
... Hi, there is one more solution to handle large data sets: the affyPara Package (http://www.bioconductor.org/packages/bioc/html/affyPara.html) You will need a computer cluster and you can do preprocessing in parallel mode. If you have enough computers you can preprocess unlimited numbers of arrays a ...
written 11.2 years ago by Markus Schmidberger380
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aroma.affymetrix and affy - different results
... Hi, I compared results from aroma.affymetrix and affy. Especially for rma background correction and quantil normalization. But there are DIFFERENCES! Any ideas for these differences? Attached my test code. Best Markus ######################################################## Code: cs <- Affym ...
normalization affy written 11.2 years ago by Markus Schmidberger380 • updated 11.2 years ago by Henrik Bengtsson2.4k
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AffyBatch -> CEL File
... Hello, is there any function or package to create a CEL File (or CEL files) from an AffyBatch? Thanks Markus -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D ...
written 11.3 years ago by Markus Schmidberger380 • updated 11.3 years ago by James W. MacDonald51k
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Error using normalize.AffyBatch.vsn()
... Hello, I get an error using "normalize.AffyBatch.vsn()" Simple Testcode and sessionInfo(): > data(affybatch.example) > a <- affybatch.example > normalize.AffyBatch.vsn(a) Fehler in validObject(.Object) : invalid class "vsnInput" object: 'subsample' must be a numeric vector of len ...
written 11.3 years ago by Markus Schmidberger380 • updated 11.3 years ago by Wolfgang Huber13k
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Error using GEOquery
... Hi, I am using the package GEOquery. But there is an error getting the GEO Series information: > gds <- getGEO("GSE2") Found 1 file(s) GSE2_series_matrix.txt.gz versuche URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2/GSE2_series_mat rix.txt.gz' ftp data connection made, file len ...
geoquery written 11.3 years ago by Markus Schmidberger380 • updated 11.3 years ago by Sean Davis21k

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