User: mai98ftu@studserv.uni-leipzig.de

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Posts by mai98ftu@studserv.uni-leipzig.de

<prev • 14 results • page 1 of 2 • next >
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Answer: A: Replicates array
... Hi Paola, For preprocessing I would suggest to use RMA (i.e. RMA background correction + quantile normalization + medianpolish) or VSN + medianpolish. I would normalize all 6 arrys together. I don't think it's a good idea to normalize the two groups separately. > Should I just compare the diffe ...
written 15.6 years ago by mai98ftu@studserv.uni-leipzig.de140
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Answer: A: problem with mva.pairs
... Francesca, I don't remember that my R session actually crashed. I think, it just takes forever. Therefore I randomly select a subset of, say, 10,000 PMs and use this subset instead: index <- sample(1:(dim(pm(myAffyData))[1]), 10000) mva.pairs(pm(myAffyData)[index,]) I don't think it's necessar ...
written 15.6 years ago by mai98ftu@studserv.uni-leipzig.de140
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Comment: C: RMA and quantile normalisation
... Arne, I'd be very surprised if you'd observe a normal distribution. You should not rely on this assumption! I haven't seen any data yet that looked like normal after RMA. However, I'm not quite sure what a more appropriate distribution would be. Johannes Quoting Arne.Muller@aventis.com: > So ...
written 15.6 years ago by mai98ftu@studserv.uni-leipzig.de140
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Answer: A: How to modify an Affybatch object?
... Puhong, The function "pm<-" should do the job. Type > help("AffyBatch-class") for more information. Johannes Quoting Puhong Gao : > Hi, all, > > Is it possible to insert the modified PM values back to the original > affybatch and then to normalize it? I'd like to use the a ...
written 15.6 years ago by mai98ftu@studserv.uni-leipzig.de140
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Answer: A: An ESR essay about software design, and how it applies to Bioconductor
... You might want to consider using commercial software with lots of pretty buttons and colorful windows to click on and with lots of black boxes crunching all the numbers for you. I, however, prefer using R and BioConductor because I don't like buttons, windows, and black boxes as much. I like to kno ...
written 15.6 years ago by mai98ftu@studserv.uni-leipzig.de140
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Answer: A: newbie question: how do I get affy annotations
... Go the BioConductor website (www.bioconductor.org) and click on "Software: How To" to get general information on how to install BioConductor packages. Then click on "MetaData". There you will find dozens of annotation packages to download and install in R. J. Quoting Hao Liu : > Dear All: &g ...
written 15.7 years ago by mai98ftu@studserv.uni-leipzig.de140
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Answer: A: a semi-legal question: linking to the BioC mailing list
... Ramon, > do I need to ask for explicit permission from every one on the linked > email? I'm not an expert on this but why would you? I mean, everyone could find those postings on her own anyway, right? So, I don't see a problem with linking to specific postings. Johannes P.S. Can you send ...
written 15.7 years ago by mai98ftu@studserv.uni-leipzig.de140
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Answer: A: Anyone Know how to make a fake CEL file?
... Hi Richard, > Does anyone know the corresponding i2xy function that would be needed > for the mu72av2 chip? as far as I know, the i2xy() function is included in the CDF packages that you can download from the BioConductor website (click on MetaData). I didn't find the respective package for ...
written 16.0 years ago by mai98ftu@studserv.uni-leipzig.de140
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Answer: A: log values of affybatch data
... Type > log.intensities <- log(intensity(affybatch.example)) Johannes Quoting Stephen Nyangoma : > Hi all, > How can I compute the logs of the Affybatch data? > > Stephen. > > _______________________________________________ > Bioconductor mailing list > Bioconducto ...
written 16.0 years ago by mai98ftu@studserv.uni-leipzig.de140
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Answer: A: Linear and spline normalization
... Hi, you can type > normalize.methods(affybatch.example) to get all the normalization methods implemented in BioConductor: [1] "constant" "contrasts" "invariantset" "loess" [5] "qspline" "quantiles" "quantiles.robust" The constant method does what Schadt et ...
written 16.0 years ago by mai98ftu@studserv.uni-leipzig.de140

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