User: Aedin Culhane

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Aedin Culhane310
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Posts by Aedin Culhane

<prev • 31 results • page 1 of 4 • next >
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Comment: C: Annotation metadata for Agilent arrays
... Thanks Everyone for your help, I got many replies. Most had built their own annotation, thinking that BioC packages had only Affymetrix annotation. However thanks a million to James who pointed to the BioC builds of Agilent annotation. There many BioC builds for Agilent chips including the human c ...
written 14.2 years ago by Aedin Culhane310
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Annotation metadata for Agilent arrays
... Hi BioC Are there metadata packages for Agilent arrays available? Thanks Aedin ...
written 14.2 years ago by Aedin Culhane310 • updated 14.2 years ago by Francois Pepin1.3k
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Removing batch effects
... Dear BioC I have a set of Affymetrix chips which have a clear "process day" batch effect. This effect is only partially removed by RMA, gcRMA, vsn or invariantset "expresso" normalisation. What would you recommend: 1. Normalize each small batch, merge the batches and re-normalize. If so is one of ...
vsn gcrma written 14.2 years ago by Aedin Culhane310 • updated 14.2 years ago by Arne.Muller@sanofi-aventis.com210
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Answer: A: PCA
... Dear Yanqin For PCA of microarary data, have a look at ord funtion in the bioconductor package made4. It simplified running PCA (and correspondence analysis) on microarray data. It takes input data in many formats including AffyBatch, ExprSet, data.frame etc. To run a PCA pca.res<- ord(data, ...
written 14.3 years ago by Aedin Culhane310
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Answer: A: how to use principal component analysis in R
... Dear Weinong, We have provided a simple package for running PCA or correspondence analysis in the bioconductor package made4. It will accept most bioconductor data classes, a matrix or data.frame. To run a PCA library(made4) res<-ord(data, "pca") plot(res) This will give a plot of the eigenvalu ...
written 14.4 years ago by Aedin Culhane310
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Comment: C: Annotation packages: Which Unigene Release?
... Thanks for the info on my last question. Can I please ask another ;-)) What do you recommend to use when mapping IMAGE ID's and Affy ID's. UniGene and locus link are returning some very strange results (not a surprise really :-)). I know match probes maps between Affy batches. Can I load IMAGE s ...
written 14.5 years ago by Aedin Culhane310
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Annotation packages: Which Unigene Release?
... Hi, I have searched the FAQ but can't find the answer to this question. How can I find out which Unigene Release was used in the creation of an annotation package. For example I am using hgu133plus2 release 1.8.4 (17th May 2005). Was this created with Unigene Release 183 or 184? Thanks a millio ...
hgu133plus2 written 14.5 years ago by Aedin Culhane310 • updated 14.5 years ago by John Zhang2.9k
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Re: Sequence alignment for DNA sequences (John Zhang)
... Hi Might also be useful to look at some of the functions in seqinR. Sorry about this, but can I ask an off topic question? Many nucleotide alignment algorithms are available. Are we replicating the effort of programs like Bioperl/EMBOSS etc etc in R? What are people's experience with RSperl and o ...
written 14.5 years ago by Aedin Culhane310 • updated 14.5 years ago by Fangxin Hong810
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Answer: A: annaffy annotation problem (hgu133plus2)
... Hi Johannes Maybe have a look at the EnsEMBL, EnsMart annotation. It permits visualization of the probe matches to the sequence which can be handy. I think your probe matches to: http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000142178 You'll prob need to follow the Affy links out from th ...
written 14.6 years ago by Aedin Culhane310
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AffyBatch: Replacing probe set IDs with Genebank
... Hi Jeppe To get from affyIDs' to genbank accession numbers: If there is a metadata package for your Affymetrix chip (you can get the metadata from the BioC website or using install.packages2()) Eg for package hgu133a library(hgu133a) Then use: hgu133aGENENAME() hgu133aACCNUM() Alternatively us ...
probe affy annbuilder written 14.7 years ago by Aedin Culhane310

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Popular Question 14.2 years ago, created a question with more than 1,000 views. For Removing batch effects

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