User: Mayer, Claus-Dieter

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Posts by Mayer, Claus-Dieter

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Comment: C: distribution of agilent array data.‏
... Hello Chunuxuan, I have worked with Agilent arrays a lot and can confirm Jim's comment the type of distribution you show (with a heavy right tail) is fairly typical. If you follow Jim's advice of smaller bin sizes/ more bins (nclass =100 or so) you will probably see that there is some mass of the d ...
written 5.9 years ago by Mayer, Claus-Dieter120
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Answer: A: Two channel data vs. one colour data for PCA, heatmaps and clustering
... Hello, One issue I found with using the single channels of a two-colour experiment in a multivariate visualisation technique (PCA plots, clustering, heatmap, etc) is that array or dye effects can mask the sources of variation you are mostly interested in. Strong array effects mean that the two chan ...
written 7.9 years ago by Mayer, Claus-Dieter120
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Comment: C: Very low P-values in limma
... Hi Paul! What can I say? Your professor is right! In one of his e-mails Gordon wrote the following: " There are some caveats. Firstly, the limma duplicateCorrelation method assumes replicates to be equally spaced, and yours are not. You've actually re-ordered your data to fit it into limma. So t ...
written 9.9 years ago by Mayer, Claus-Dieter120
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Comment: C: Very low P-values in limma
... Dear Paul! What is the corfit$consensus value? If it is close to 1, using limma with duplicateCorrelation or averaging (or indeed just using any of the duplicates) should give you very similar results. If however corfit$consensus is close to 0, limma would indeed treat the duplicates similar to ind ...
written 9.9 years ago by Mayer, Claus-Dieter120
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Comment: C: question about topTable ranking of limma
... Hi, With only one group you can not speak of "differentially expressed" and testing, as that assumes that you have at least two different groups or conditions. The test that you have performed probably just compares gene expression to zero (a moderated one-sample t-test) and for that you would expe ...
written 10.0 years ago by Mayer, Claus-Dieter120
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Comment: C: Array Set - Multiple Testing Problem
... Hello, I might have misunderstood something, but assuming such an array set consists of k arrays, wouldn't it be the easiest to perform k normalizations and analyses which give you k lists of p-values for k (non-overlapping (I assume!?)) sets of genes. To adjust for multiple testing you need to bi ...
written 10.0 years ago by Mayer, Claus-Dieter120
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Answer: A: Question regarding Affy SNP 5.0/BI_SNP arrays
... Dear Benilton! Thanks for your answer. I was aware that you can specify the package name. If I use the option 'pkgname="pd.genomewidesnp.5"' my R console crashes under windows and gives me endless error messages ("caught segfault: address Oxd, cause unknown" under Linux, while it all works fine wit ...
written 10.4 years ago by Mayer, Claus-Dieter120
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Question regarding Affy SNP 5.0/BI_SNP arrays
... Dear all! A collaborator asked me to help her with the analysis of some Affy SNP 5.0 arrays they obtained from the AGRE projecet (a huge database collecting many datasets concerning Autism Genetics). I have to admit that I am pretty much a novice when it comes to SNP- arrays, so I started with taki ...
snp annotation cdf affy process oligo written 10.4 years ago by Mayer, Claus-Dieter120 • updated 10.4 years ago by Williams, Alan40
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Comment: C: Problem with p-values calculated by eBayes--corrected format
... Hi Zhuoxun Chen! As Kasper indicates below there might be a combination of reasons for the difference you observe but one of them is in fact quite easy to explain. One of the main differences between the limma version of a t-test with the standard t-test is the standard of difference (SED), which o ...
written 10.7 years ago by Mayer, Claus-Dieter120
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Comment: C: Normalized microarray data and meta-analysis
... Dear Tom, That is an interesting point you make (and interesting paper you refer to) but in my view it is not the main aim of a meta-analysis to find the concordance between the individual studies but to summarize these studies in such a way that you have a higher power/sensitivity than any of the ...
written 10.8 years ago by Mayer, Claus-Dieter120

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