Dear BioC, Here is my R script code which is running on server in background. ################################## chiptype <- annotation(affy_batch_object); if(chiptype == "hu6800") { library(hu6800cdf); library(hu6800probe); library(hu6800); library(humanCHRLOC); library(humanLLMappings); envGeneNames <- hu6800GENENAME; # very important envPath2Probes <- hu6800PATH2PROBE; envGO2AllPROBES <- hu6800GO2ALLPROBES; envGENEIDS <- hu6800ENTREZID; # very important } and so on for commonly used AFFY Chips.... ################################## I have written this manually, how can I load annotations and packageENGREZID, packageGENENAME..etc. dynamically? I am currently working with Affy chips but I also like to work on Agilent chips in futureI. OR I just write a perl/php scripts which prints above information...thats my thinking. Thank you so much in advance, Saurin |------------------------------------------------ | Saurin D. Jani | Bioinformatician | | Department of Cell Biology and Anatomy | Medical University of South Carolina (MUSC) | 173 Ashley Ave | Charleston,SC - 29425 | | Email: jani at musc.edu | Phone: (843)792-1340 | Website: http://www.musc.edu/~jani |------------------------------------------------

On Sat, Sep 27, 2008 at 9:57 AM, Jani, Saurin D <jani at="" musc.edu=""> wrote: > Dear BioC, > > Here is my R script code which is running on server in background. > ################################## > chiptype <- annotation(affy_batch_object); > > if(chiptype == "hu6800") > { > library(hu6800cdf); > library(hu6800probe); > library(hu6800); > library(humanCHRLOC); > library(humanLLMappings); > envGeneNames <- hu6800GENENAME; # very important > envPath2Probes <- hu6800PATH2PROBE; > envGO2AllPROBES <- hu6800GO2ALLPROBES; > envGENEIDS <- hu6800ENTREZID; # very important > } > > and so on for commonly used AFFY Chips.... > ################################## > > I have written this manually, how can I load annotations and packageENGREZID, packageGENENAME..etc. dynamically? > > I am currently working with Affy chips but I also like to work on Agilent chips in futureI. Hi, Saurin. You didn't give your sessionInfo(), but you will want to be using the .db packages and R-2.7 if possible, since those are now the standard for distributing annotation packages. You can look at the AnnotationDbi package vignette for details. That said, this will work for the older environment-base packages, if you like, thanks to the environment API. > annot <- 'hu6800' > l <- paste(annot,'.db',sep="") > library(l,character.only=TRUE) > geneNames <- as.list(get(paste(annot,'GENENAME',sep=""))) > geneNames[1:5] $A28102_at [1] "gamma-aminobutyric acid (GABA) A receptor, alpha 3" $AB000114_at [1] "osteomodulin" $AB000115_at [1] "interferon-induced protein 44-like" $AB000220_at [1] "sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C" $AB000381_s_at [1] "glycosylphosphatidylinositol anchored molecule like protein" > geneIDs <- as.list(get(paste(annot,'ENTREZID',sep=""))) > geneIDs[1:5] $A28102_at [1] "2556" $AB000114_at [1] "4958" $AB000115_at [1] "10964" $AB000220_at [1] "10512" $AB000381_s_at [1] "2765" > I just write a perl/php scripts which prints above information...thats my thinking. You could certainly do that, also, but I challenge you to do what was done above in 4 lines of code. : ) Sean