Moderator: Rafael A. Irizarry

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Posts by Rafael A. Irizarry

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Can't reproduce assessment data included in affycomp package
... Philippe, Thanks for catching this. And sorry it took so long to reply. We have been busy fixing the problem. Here is what happened: In 2004 we made a change to one of the assessment functions. Specifically, the definition of low, medium and high strate changed for the fold change assessments. Unfo ...
cancer affy affycomp process safe written 6.2 years ago by Rafael A. Irizarry2.3k • updated 6.2 years ago by Harris A. Jaffee590
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Job postings
... http://www.biostat.jhsph.edu/employment/postdoc.html ...
written 8.8 years ago by Rafael A. Irizarry2.3k
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Analysis of Affy-data from amplified RNA
... Samuel, Thanks for the note. Regarding your request I would recommend you start with the bioconductor mailing list for help: bioconductor Mailing List Best wishes, Rafael Samuel Wuest wrote: > Dear Rafa, > > Hope you are fine? I have become a big fan of you when I came across the > ...
probe roc written 9.7 years ago by Rafael A. Irizarry2.3k
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postdoc opportunities
... If you are interested in a postdoc position please ssee: http://www.biostat.jhsph.edu/employment/ Best wishes, Rafael ...
written 9.9 years ago by Rafael A. Irizarry2.3k
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Comment: C: symbol to location
... perfect. thanks -r On Tue, 26 Dec 2006, Steffen Durinck wrote: > Hi Rafa, > > You can do this easily with biomaRt, here's the code: > > library(biomaRt) > ensembl=useMart("ensembl",dataset="hsapiens_gene_ensembl") > symbols = c("AATK","ABCB1") > getBM(c("hgnc_symbol","chro ...
written 10.8 years ago by Rafael A. Irizarry2.3k
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symbol to location
... Hi! Can you recommend your favorite way to go from gene symbols, such as AATK, ABCB1, etc.. to genomic location? what ive come up with seems way to cumbersome. -r ...
go written 10.8 years ago by Rafael A. Irizarry2.3k • updated 10.8 years ago by Steffen Durinck580
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Answer: A: scale of mas5, rma, dchip, and plier results
... rma-log2 mas5-original dchip-original (i think) as a general rule if the scale is around 0 to 16 its log2 if its around 0 to 40000 its original scale. On Thu, 24 Aug 2006, He, Yiwen (NIH/CIT) [C] wrote: > Hi, > > > > I'm trying to compare the probe level data analysis tools includ ...
written 11.1 years ago by Rafael A. Irizarry2.3k
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Comment: C: questions about RLMM
... Yen-Tsung, As Jim points out the oligo package can handle this data. The "crlmm" function will implement a calling algorithm we have just finished fine-tunning. You can read about it here: http://www.bepress.com/jhubiostat/paper111/ Documentation is still under development so if you want to try i ...
written 11.2 years ago by Rafael A. Irizarry2.3k
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breast tissue cel files
... Hi all! I am looking for cel file obtained from hybing normal breast tissue to the hgu133a array. We could not find anything on GEO or ArrayExpress. Suggestions on where to find some will be greatly appreciated. Rafael ...
hgu133a arrayexpress written 11.2 years ago by Rafael A. Irizarry2.3k
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Comment: C: Normalization of 2 color Nimblegen array
... Hi! I just wanted to point out that the oligo package supports nimblegen arrays (you need the xys and ndf) files. It is under development but we need testers. If anybody wants a specific method or function incorporated you can email benitlon or me. Most functions in the affy package can be easily ex ...
written 11.5 years ago by Rafael A. Irizarry2.3k

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