I've struggled with makeProbePackage for a while now, working with my Probe, and getting nothing. Any attempt to use the probe packages I made would end up with //"Computing affinitiesError: length(prlen) == 1 is not TRUE". //That would be using this as a script: ---------------------8<----------------------------------------- library(matchprobes) filename <- system.file( "extdata" , "AFLAVUSa520391F_probeseqs.txt" ) outdir <- '.' species <- 'Aspergillus_flavus' me <- "Dave Jacoby <jacoby at="" purdue.edu="">" makeProbePackage( "AFLAVUSa520391F" , datafile = filename , outdir = outdir , species = species , maintainer = me , version = '0.0.1' , force = TRUE ) ---------------------8<----------------------------------------- But there's a one-line fix that I've found. Replacing filename <- system.file( "extdata" , "AFLAVUSa520391F_probeseqs.txt" ) with filename <- list.files( pattern = "probeseqs.txt" ) gave me a working probe package for the first time. I hope this helps somebody. -- David Jacoby jacoby at purdue.edu Purdue Genomics Facility S049, WSLR building Phone: hah!

Hi Dave, Dave Jacoby wrote: > I've struggled with makeProbePackage for a while now, working with my > Probe, and getting nothing. > Any attempt to use the probe packages I made would end up with > //"Computing affinitiesError: length(prlen) == 1 is not TRUE". > > //That would be using this as a script: > > ---------------------8<----------------------------------------- > library(matchprobes) > > filename <- system.file( "extdata" , "AFLAVUSa520391F_probeseqs.txt" ) > outdir <- '.' > species <- 'Aspergillus_flavus' > me <- "Dave Jacoby <jacoby at="" purdue.edu="">" > makeProbePackage( "AFLAVUSa520391F" , > datafile = filename , > outdir = outdir , > species = species , > maintainer = me , > version = '0.0.1' , > force = TRUE ) > ---------------------8<----------------------------------------- > > But there's a one-line fix that I've found. Replacing > > filename <- system.file( "extdata" , "AFLAVUSa520391F_probeseqs.txt" ) > > with > > filename <- list.files( pattern = "probeseqs.txt" ) > > gave me a working probe package for the first time. I hope this helps > somebody. Yes. That is a problem with blindly following the example from a help page without understanding what it does. Since the example is expected to run and the only way for that to be true is to supply the example with a probe_tab file, there is a small file in the package itself that is used for that purpose. By calling system.file() the example will be able to find that file without having to explicitly state where it might be (which will vary depending on the OS and any personal libraries that may exist). The canonical way to call makeProbePackage() doesn't even involve the datafile argument (which you can see isn't listed in the arguments section of the help page). All you need is something like: makeProbePackage("AFLAVUSa520391F", species="Aspergillus_flavus", version="0.01", maintainer="Dave Jacoby <jacoby at="" purdue.edu="">", force=TRUE, check=FALSE, build=FALSE) This is the downside of having a workable example for a function that requires external data -- for the example to work you often need to utilize extra gymnastics that the end user won't need and arguably shouldn't emulate. Best, Jim > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623