User: Hinnerk Boriss

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Posts by Hinnerk Boriss

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Answer: A: normalization for custom chip
... Dear Shibing, I do not recommend using house keeping genes for normalization. In several experiments they turn out being differentially expressed. A better approach would be to use a normalization method that searches for an invariant set of genes in the sample. "VSN" and Li & Wong's "invariant ...
written 15.1 years ago by Hinnerk Boriss220
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Installation of version 1.4: vsn
... Hi, I tried to install the new version 1.4, however, noticed that neither the default (getBioC() ) nor explicitly calling getBioC("cdna") would install the vsn library. That is confusing as the installation instructions say that this should work. How can that be fixed? Best regards, Hinnerk ...
vsn written 15.5 years ago by Hinnerk Boriss220 • updated 15.5 years ago by Johannes Freudenberg30
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Answer: A: multtest on human intervention study
... Hi Kevin, did you do in vitro amplification of your samples to increase the cRNA available for hybridization? This is a common source of the problem you are describing. There are no mathematical methods for retrofixing this problem. > Q1: Do you have any arguments against the RMA(after)-RMA(befo ...
written 16.0 years ago by Hinnerk Boriss220
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Annotation package for Drosophila chip
... Hi there! Has anyone build the annotation package for Affymetrix drosgenome1 chip? If so, would you share? Many thanks in advance. Cheers, Hinnerk ...
annotation written 16.0 years ago by Hinnerk Boriss220 • updated 16.0 years ago by John Zhang2.9k
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Comment: C: Advice for analyzing Affy data
... Hi! the Tuckey bigweight summary stat method (mas) does no data transformation when raw values are supplied in the AffyBatch object, however, it magically transforms the data when they are log or arcsinh transformed. What transformation is used? Where could I find out myself? And is there a why (op ...
written 16.2 years ago by Hinnerk Boriss220
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Comment: C: se.exprs
... Hi, I've been experimenting with the heatmap function of the mva library and am not happy with the ordering I get. Does anyone have a good suggestion? Or could you point me to a documentation of Jonathan Eisen's ordering algorithm? Many thanks in advance, Hinnerk ...
written 16.4 years ago by Hinnerk Boriss220
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Comment: C: LocusLink query problem / bioC basic tutorial
... > > for teaching purposes I would like to cut down the number > of genes in > > affybatch objects so that students won't have to wait that long for > > their computations. Unfortunately, I cannot figure out how > to do that. > > Any hints? Thanks! > > Cutting down ...
written 16.5 years ago by Hinnerk Boriss220
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Comment: C: LocusLink query problem / bioC basic tutorial
... > i'd like to add there is a simple way to remove genes. its > not the best > way but its simple and itll do the trick: > say ab is your affybatch and hgu95acdf is your cdf before > your class type: > > 1) library(hgu95acdf) #probably already loaded > 2) takeout <- ls(hgu ...
written 16.6 years ago by Hinnerk Boriss220
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Answer: A: LocusLink query problem / bioC basic tutorial
... Hi there, for teaching purposes I would like to cut down the number of genes in affybatch objects so that students won't have to wait that long for their computations. Unfortunately, I cannot figure out how to do that. Any hints? Thanks! Yours dreaming of good old plob objects, Hinnerk ...
written 16.6 years ago by Hinnerk Boriss220
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Answer: A: Affy RNA digestion plots (fwd)
... Hi! What does the p-value of the RNA degradation test actually say and where do things begin to become critical? For instance, I have data here where the p-values are rather low (hgu133A chips) and in fact the slopes are positive! What is the appropriate interpretation? No RNA degradation? Somethin ...
written 16.7 years ago by Hinnerk Boriss220

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