User: Claus Mayer

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Claus Mayer330
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Posts by Claus Mayer

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Pathway Analyis for C-difficile microarrays
... Hello! I am working on a data set using C-difficile two-color microarrays and would like to do some pathway analysis. KEGG has quite a number of pathways for this organism (see http://www.genome.jp/kegg- bin/show_organism?menu_type=pathway_maps&org=cdf), but when I tried to access them with KEG ...
organism written 8.7 years ago by Claus Mayer330
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Comment: C: Reg: T-statistic using limma
... That Venn Diagram is not very interesting in your case. The intercept will (unless you centered the data for some reason) always be significant and is of little interest. The comparison you are interested is between the groups. The empty circle in the diagram just means that you have no genes signi ...
written 9.7 years ago by Claus Mayer330
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Answer: A: Reg: T-statistic using limma
... It should be population.goups <- factor(c(rep("LL",3),rep("Control",3)) The way you defined it, each array forms his own group (and thus you have no degrees of freedom left). Claus > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bo ...
written 9.7 years ago by Claus Mayer330
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Answer: A: Limma and logistic regression
... Hi Dan! I am sure there are better references for this but you can find some discussion on the topic logistic regression vs t-test at this link: http://udel.edu/~mcdonald/statlogistic.html . In an ideal world you assume in a regression model that the explanatory variable is fixed by the experiment ...
written 9.7 years ago by Claus Mayer330
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Comment: C: FW: duplicates, technical and biological replicates + dividing a microarray into
... Dear Ana, To give Naomi some rest, perhaps I can help with some answers: > > 1. Now that you mention, I can see that the within array variability > should be smaller then the technical variability, > but I cannot understand why treating them as the same, should be less > statistica ...
written 9.8 years ago by Claus Mayer330
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Answer: A: MA plots + dye swap
... Hi Guido! Additionally to what Wolfgang already wrote you might have a look at a related thread on the mailing list, that was discussed just recently (https://stat.ethz.ch/pipermail/bioconductor/2010-January/thread.html# 31254) . What you call "mirrored version" of the MA-Plot, corresponds to the ...
written 9.9 years ago by Claus Mayer330
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Answer: A: Package on clinical data analysis
... Hi David! I haven't had many data sets like that but as far as I can see limma is not only capable of comparing groups but you can also have continuous measurements as explanatory variables, i.e. fit a multiple regression type of model by defining the design as Design<- model.matrix(~ var1 + va ...
written 9.9 years ago by Claus Mayer330
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Answer: A: Positive correlation between dye-swap technical replicates
... Dear Michal! You should include dye effect in your linear model (cf the limma guide 8.1.2 Dye Swaps). The normalization only removers an overall dye-effect but typically that effect is slightly different from gene to gene. Including the dye effect in the model should remove this remaining gene-spec ...
written 9.9 years ago by Claus Mayer330
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Answer: A: globaltest mulitple testing correction
... Hello Michael, I think there are some things you are confusing here. It is correct that SAM uses a permutation method to give q-values, i.e.estimates of the FDR one would obtain when thresholding at the given value of the test-statistic. This is SAM's specific way of using the permutations though. ...
written 11.1 years ago by Claus Mayer330
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Comment: C: Question about F test in limma
... Dear Lisa, no this is not a chance finding. Whether you include all 3 possible contrasts or just the two you specify below: if all contrasts are zero this is equivalent to the overall null hypothesis that all 3 treatment means are the same, i.e. the F-test is testing the same hypothesis in both ca ...
written 11.6 years ago by Claus Mayer330

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