User: Arne.Muller@aventis.com

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Posts by Arne.Muller@aventis.com

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Dose-Response: Regressiion and ANOVA
... Dear All, I'm interested in your experience of analyzing dose-response experiments. I've an unbalanced design with 3 studies and within each study 4 to 5 doses of a drug (the doses do not exactmy the same in each study). Usually I run an anova per gene anova(lm(Intensity ~ Study + Dose + Study:Do ...
regression dose written 12.9 years ago by Arne.Muller@aventis.com620 • updated 12.9 years ago by Liaw, Andy360
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normalizaton between studies
... Dear All, I'd like to continue on the topic I've posted a few daysa go ("unbalanced design") - but in a slightly different direction ... I'm trying to figure out a dose response from an experiment (affy) that was conducted in three independent studies (basically each study conducted the same dose ...
normalization vsn dose written 13.0 years ago by Arne.Muller@aventis.com620 • updated 13.0 years ago by Anja.von.Heydebreck@merck.de10
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unbalanced design
... Dear All, I'm wondering which method to use to analyse a rather unbalanced design (Affy). I've three studies (S1..S3) in which several doses of a drug have been tested. The table blow gives the number of observations (the replicates, cell cultures) per study/dose combination: S1 ...
limma dose written 13.0 years ago by Arne.Muller@aventis.com620 • updated 13.0 years ago by Gordon Smyth32k
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normalisation or analysis with batch effects
... Hello, the 11 tumour sampel are considered as biological replicates, or are these split into different tumour classes? We've had a similar problem. Our data was generated in three different laboratories, each having slightly different protocols, but within each lab we had the same factors (the sam ...
cancer written 13.0 years ago by Arne.Muller@aventis.com620
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Answer: A: Installing Packages from Bioconductor: Error
... Hi Eric, Maybe you're behind firewall that needs authentification? In this case you may have to start R as "C:\Program Files\R\rw1090\bin\Rgui.exe" --internet2 right-click on the R-icon on your desktop and modify the properties to use --internet2 (this uses the same internet connection API as in ...
written 13.0 years ago by Arne.Muller@aventis.com620
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excluding absent genes - again
... Hello, I remember some discussions a while ago whether to exclude "absent" genes(potentially non-expressed as determined by MAS5 p-values etc...) from the down stream statistical analysis. This was/is quite a debate. Can anybody point out a paper reviewing this issue? kind regards, ...
written 13.2 years ago by Arne.Muller@aventis.com620
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Answer: A: Normalising divergent samples.
... Hello, I'm not sure wheather my comment fits in precisely. I'm writing up a toxicology study for which gene expression was measured by three independent laboratories for a compound at different doses. The dose effet is rather small (~200 genes effected at p < 0.001) but at least half of the gen ...
written 13.2 years ago by Arne.Muller@aventis.com620
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Friedman test
... Hello, I've a rather statistical question ... I've an experimental design with 2 factors, batch (3 levels) and dose (5 levels) with 0 to 4 technical replicates (a dose is missing for a certain batch). I've seen that one batch has consistently lower variance within doses for most of the genes I've ...
dose written 13.2 years ago by Arne.Muller@aventis.com620
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GOStat and multiple testing
... Hello, I was wondering if one needs to correct the p-values from the hypergeometirx test from GOstat for mutliple testing, since one performs many tests (over all GO categories found in the gene list). I'm not sure if correction for multiple testing makse sense since the GO terms are highly depende ...
go gostats written 13.3 years ago by Arne.Muller@aventis.com620 • updated 13.3 years ago by A.J. Rossini810
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correlation image and tickmarks
... Hello, I've a problem aligning tickmarks to an image. I've created a correlation matrix for 84 affy mouse chips. I'm visualizing the matrix as an image with colour coding according to the correlation coefficient. The 84 chips are distributed over three factors, but the desgin is unbalanced, so tha ...
affy written 13.3 years ago by Arne.Muller@aventis.com620

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