User: Gunther Höning

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Posts by Gunther Höning

<prev • 10 results • page 1 of 1 • next >
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Comment: C: a bug in hypergraph?
... Dear list, is it possible to use functions provided in Bioconductor (e.g. gcrma, affybatch, vns...) in C? Or calling these functions from C? Wishes Gunther ...
written 11.8 years ago by Gunther Höning100
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Comment: C: lumiT VST error
... Dear list, I'm looking for the source codes for affy,gcrma and quantiles. Can anyone tell me where to find themn ? Gunther -----Urspr?ngliche Nachricht----- Von: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag von Pan Du Gesendet: Donnersta ...
written 12.4 years ago by Gunther Höning100
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Comment: C: ReadAffy gives Error
... Hi, I had no problems reading and analyzing about 55 hgu133plus2 chips on an intel-based 32bit opensuse 10.2 system and 4 GB RAM. But for more chips I intent to use a 64bit linux with a minimum of 16 GB RAM. Gunther -----Urspr?ngliche Nachricht----- Von: bioconductor-bounces at stat.math.ethz.ch ...
written 12.7 years ago by Gunther Höning100
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Comment: C: Memory error wihle processing 35 Affymetrix cel files
... Dear list, as I mentioned in my task before (Memory error while processing 35 Affymetrix cel files) I analyze a lot of data. My own processing steps after bg-correction and normalization will (hopefully) improve the cel files I have. So I am looking for an suitable workstation configuration, e.g. 6 ...
written 12.7 years ago by Gunther Höning100
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Answer: A: Memory error wihle processing 35 Affymetrix cel files
... Thanks for your suggestions, but I want to use my own summarization thus I only need the first two steps of array analysis. BG-correction and normalisation. data <- ReadAffy() eset <- bg.adjust.gcrma(data) eset.norm <- normalize(eset, method ="quantiles") .. and so on... So I can't use ju ...
written 12.7 years ago by Gunther Höning100
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Answer: A: Error in RankProd package
... Dear list, currently I'm trying to process 35 cel-files of the Affymetrix Human U133 Plus 2.0 chip. I load the libraries and read the chips into an affybatch. Background correction works well but during normalisation I always receive: "Cannot allocate vector of size 352848...") I am using openlin ...
written 12.7 years ago by Gunther Höning100
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Affy! From raw data files to Summary expression value without expresso!
... Dear list, I calculated correction values for each probe cell. I do the following: Reading the cel-files in an AffyBatch: Expfiles <- c("1.CEL","2.CEL","3.CEL","4.CEL") chips = ReadAffy(filenames = Expfiles) Performing background correction: Chips.bg.mas <- bg.correct(chips, method ="mas") ...
probe written 13.0 years ago by Gunther Höning100 • updated 13.0 years ago by James W. MacDonald52k
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Question on read.probematix
... Dear list, I have a short question on read.probematrix(). I use an Affymetrix hgu133plus2 chip. It has 1164 rows and 1164 columns. Thus I expect 1354896 (=1164*1164) messured intensity points. But reading a cel-file I receive 2 (pm and mm) * 604258 = 1208516 entries. The difference is 146380. Even ...
hgu133plus2 written 13.2 years ago by Gunther Höning100 • updated 13.2 years ago by James W. MacDonald52k
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Comment: C: Question on AffyBatch
... Hi, that's exactly what I was looking for. Thanks. Gunther -----Urspr?ngliche Nachricht----- Von: Wolfgang Huber [mailto:huber at ebi.ac.uk] Gesendet: Donnerstag, 7. September 2006 07:50 An: Gunther H?ning Cc: bioconductor at stat.math.ethz.ch Betreff: Re: [BioC] Question on AffyBatch Gunther H ...
written 13.3 years ago by Gunther Höning100
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Question on AffyBatch
... Dear list, I'm trying to find out the following in an AffyBatch. To get the indices from a loction on a chip I use the function xy2i() for the hgu133plus2 by Affymetrix. But now I want to know the name of the probe located at this spot. How can this be done? And what about the locations used as QC ...
hgu133plus2 probe written 13.3 years ago by Gunther Höning100 • updated 13.3 years ago by Wolfgang Huber13k

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