User: Georg Otto

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Georg Otto510
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Posts by Georg Otto

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limma design question - technical replicates
... Hi, I have a question about dealing with a design that is a mixture of technical and biological replicates. It's 4 two color-arrays with the dye-swap structure: 1,-1,1,-1 array 3 and 4 are technical replicates of the same biological source, so the biological replicate structure is: 1,2,3,3 Thi ...
written 9.8 years ago by Georg Otto510
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Answer: A: variable as argument to makeContrasts (limma)
... Martin Morgan writes: > Georg Otto wrote: >> Martin Morgan >> writes: >> >>> One way is to aim for >>> >>> do.call(makeConstrasts, myargs) >>> >>> where the 'myargs' is a list that you can construct any way you >>> like ...
written 9.8 years ago by Georg Otto510
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Answer: A: variable as argument to makeContrasts (limma)
... Martin Morgan writes: >> >> Georg Otto wrote: >>> Hi, >>> >>> maybe this is a more general R programming question, but I first try it >>> here, because the problem occured to me with limma: >>> >>> I use the function makeContrasts ...
written 9.8 years ago by Georg Otto510
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variable as argument to makeContrasts (limma)
... Hi, maybe this is a more general R programming question, but I first try it here, because the problem occured to me with limma: I use the function makeContrasts makeContrasts(...,levels=design) like this makeContrasts(B-A,C-B,C-A,levels=design) now instead of giving explicitely "B-A,C-B,C-A" ...
written 9.8 years ago by Georg Otto510
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problem using annotation database with annaffy
... Hi, I built an annotation package for the Agilent zebrafish array and used this in combination with annaffy to generate text files and html with expression data and annotations. This used to work fine before I upgraded to R 2.9 and bioconductor 2.4. Now, i get an error: > library(annaffy) > ...
annotation go zebrafish annaffy written 9.8 years ago by Georg Otto510
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Answer: A: Visualise KEGG pathway and highlight genes
... Hi Daniel, Daniel Brewer writes: > >>From a couple of interesting gene lists I have found KEGG pathways which > contain genes from both lists. Does anyone know how to visualise this? > I was thinking something along the lines of the KEGG pathway being > plotted and the genes f ...
written 9.9 years ago by Georg Otto510
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limma warning: Estimation of var.prior failed
... Hi, I am processing a set of around 40 Affymetrix hybridizations of (I think) quit good quality. When I run limma on the rma-normalized set, everything runs smoothly. > fit<-lmFit(eset.rma, design) > fit<-eBayes(fit) However when I do the same thing on the gcrma-normalized set, I rec ...
go limma written 10.6 years ago by Georg Otto510
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Answer: A: agilent zebrafish array annotation
... Marc Carlson writes: > Georg Otto wrote: >> Hi, >> >> I started to use the agilent zebrafish array and I am using >> bioconductor packages (limma and others) for the data analysis as I >> did already with the Affymetrix zebrafish array. I noticed that unlike >&g ...
written 10.9 years ago by Georg Otto510
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agilent zebrafish array annotation
... Hi, I started to use the agilent zebrafish array and I am using bioconductor packages (limma and others) for the data analysis as I did already with the Affymetrix zebrafish array. I noticed that unlike for the Affymetrix zebrafish array, there is no annotation package for the Agilent zebrafish arr ...
annotation zebrafish annbuilder process annotationdbi written 10.9 years ago by Georg Otto510
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Answer: A: How to perform annotation using refseq IDs and GO ?
... Hi, if your organism is in the Ensembl database, you can use the biomaRt package to retrieve GO annotations. biomaRt is explained quite nicely in www.stat.berkeley.edu/~steffen/BioC2007-biomaRt.pdf For example, if geneids.rm is a vector of RefSeq RNA ids, you can retrieve the associated GO anno ...
written 11.1 years ago by Georg Otto510

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