## User: Kasper Daniel Hansen

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k*******@biostat.ku.dk

#### Posts by Kasper Daniel Hansen

<prev • 63 results • page 1 of 7 • next >
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... Just to be really clear, what we are talking about is an interface to http://www.affymetrix.com/support/developer/filesdk/index.affx?terms=n o which is a C++ library which can parse CEL, CHP, CDF, BPMAP, BAR files. Several of these file formats are already readable by BioC, but I still think it is ...
written 14.5 years ago by Kasper Daniel Hansen630
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... Is there really no-one who thinks it is a good idea to integrate the Affymetrix SDK for reading various file formats, into Bioconductor? Kasper On Sat, May 21, 2005 at 10:58:19AM -0700, James Bullard wrote: > > Hi all, we have been working for the last month or so on integrating the > Aff ...
written 14.5 years ago by Kasper Daniel Hansen630 • updated 14.5 years ago by Seth Falcon7.4k
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Comment: C: as.numeric and NA
... What Wolfgang is implying is that it is a rather strange thing you want to do. Your command was as.numeric(sampleNames(data.raw)) with data.raw an AffyBatch object. Now, sampleNames(data.raw) will return you a vector of sampleNames, which is a character vector with names associated with each sam ...
written 14.5 years ago by Kasper Daniel Hansen630
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... It could in principle be scritable and might even be a little worthwhile to do it. But basically the BioC version number is corresponds to a whole list of individual package numbers. As sson as you move away from the getBioC script you can have a big mix of development and release level packages. K ...
written 14.6 years ago by Kasper Daniel Hansen630
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... It seems that you want to summarize the probe intensities into a single numbr for each gene. This is not what I would consider "raw" data. Furthermore there is no transformation which is inheirently more "raw" than others. I think you need to read up a bit on summarizing methods. In case you want t ...
written 14.6 years ago by Kasper Daniel Hansen630
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... On Fri, May 06, 2005 at 06:14:34AM -0400, Sean Davis wrote: > zraw.normrg$M[(zraw$R<200) | (zraw\$G<200)] <- NA The preferred way is to use is.na(x) <- TRUE ...
written 14.6 years ago by Kasper Daniel Hansen630
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... read.affybatch reads the file into an AffyBatch object. This object is very similar to an exprSet, and there is no normalization or anything going on. Afterwards you can use exprs() to acces the raw expression intensities. Kasper On Fri, May 06, 2005 at 08:34:27AM +0200, s_r wrote: > Hi. > & ...
written 14.6 years ago by Kasper Daniel Hansen630
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Comment: C: End2End Lab Material
... On Wed, May 04, 2005 at 06:53:36AM -0700, Seth Falcon wrote: > Hi Cecilia, > > Cecilia Fernandez writes: > > I am a beginner with Bioconductor, and I was trying to use the lab > > material End2End, but it asks for a library called "bioclads". When I > > try to use it I ge ...
written 14.6 years ago by Kasper Daniel Hansen630
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... Yes, use > gc() It should be called automatically when needed (I think), but I must say I get better results by calling it manually immediately after deleting massive datasets. Kasper On Wed, May 04, 2005 at 08:55:36AM +0200, Dipl.-Ing. Johannes Rainer wrote: > hi, > is there some kind of ...
written 14.6 years ago by Kasper Daniel Hansen630
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... Of the 16 members of R core, 5 are members of Bioconductor core. I do not think that you need to worry that there is no communication. Many changes in R in the last years have been initiated because of Bioonductor. And according to Seth (I have not yet looked at it myself), R's installation routines ...
written 14.6 years ago by Kasper Daniel Hansen630

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