Sorry to bother the list with what is probably a dumb question. I looked in the list archives and online, and in the code for the routines ReadAffy and read.affybatch, and for the life of me, I can't figure it out. I used library(makecdfenv) to create an alternative CDF environment where I mask out some probes in a probeset, and I try to load it into an affyBatch, and I get... > library(PHYH) > ReadAffy(verbose=TRUE,cdfname=PHYH) 1 reading /home/tim/Hacia/cb1.cel ...instantiating an AffyBatch (intensity a 1354896x55 matrix)...done. Reading in : /home/tim/Hacia/cb1.cel Reading in : /home/tim/Hacia/cb2.cel Reading in : /home/tim/Hacia/cb3.cel ... Reading in : /home/tim/Hacia/ht6.cel Error in as.character(args[[i]]) : cannot coerce to vector > Any suggestions? I can't figure out what's going on here. I have loaded plenty of affyBatch'es of CEL files before, but never with an alternatively masked CDF environment... when I do it like so, > ReadAffy(verbose=TRUE) 1 reading /home/tim/Hacia/cb1.cel ...instantiating an AffyBatch (intensity a 1354896x55 matrix)...done. Reading in : /home/tim/Hacia/cb1.cel Reading in : /home/tim/Hacia/cb2.cel Reading in : /home/tim/Hacia/cb3.cel ... * Installing *source* package 'hgu133plus2cdf' ... ** R ** data ** help >>> Building/Updating help pages for package 'hgu133plus2cdf' Formats: text html latex example geometry text html latex example hgu133plus2cdf text html latex ** building package indices ... * DONE (hgu133plus2cdf) The downloaded packages are in /tmp/RtmpIMTi6e/downloaded_packages Attaching package: 'hgu133plus2cdf' The following object(s) are masked from package:PHYH : i2xy The following object(s) are masked from package:PHYH : xy2i AffyBatch object size of arrays=1164x1164 features (582203 kb) cdf=HG-U133_Plus_2 (54675 affyids) number of samples=55 number of genes=54675 annotation=hgu133plus2 ... it works OK. So should I unpack the hgu133plus2cdf package, mask out probes (merge into a custom CDF), and then use that? Seems like I am missing something obvious here. Need more eyes! Much obliged, thank you in advance for your helpful advice, --tim -- "People seldom do what they believe in. They do what is convenient, then repent." --Bob Dylan

Hi Tim, Tim wrote: > Sorry to bother the list with what is probably a dumb question. > > I looked in the list archives and online, and in the code for the > routines ReadAffy and read.affybatch, and for the life of me, I > can't figure it out. I used library(makecdfenv) to create an > alternative CDF environment where I mask out some probes in a > probeset, and I try to load it into an affyBatch, and I get... We will need more information before anybody will be able to help. First, how exactly did you use makecdfenv to create an alternative CDF environment? Second, what do you get when you do traceback() after the error? Third, what is your sessionInfo()? Best, Jim > > >>library(PHYH) >>ReadAffy(verbose=TRUE,cdfname=PHYH) > > 1 reading /home/tim/Hacia/cb1.cel ...instantiating an AffyBatch > (intensity a 1354896x55 matrix)...done. > Reading in : /home/tim/Hacia/cb1.cel > Reading in : /home/tim/Hacia/cb2.cel > Reading in : /home/tim/Hacia/cb3.cel > ... > Reading in : /home/tim/Hacia/ht6.cel > Error in as.character(args[[i]]) : cannot coerce to vector > > > > Any suggestions? I can't figure out what's going on here. I have > loaded plenty of affyBatch'es of CEL files before, but never with an > alternatively masked CDF environment... when I do it like so, > > >>ReadAffy(verbose=TRUE) > > 1 reading /home/tim/Hacia/cb1.cel ...instantiating an AffyBatch > (intensity a 1354896x55 matrix)...done. > Reading in : /home/tim/Hacia/cb1.cel > Reading in : /home/tim/Hacia/cb2.cel > Reading in : /home/tim/Hacia/cb3.cel > ... > * Installing *source* package 'hgu133plus2cdf' ... > ** R > ** data > ** help > >>> Building/Updating help pages for package 'hgu133plus2cdf' > Formats: text html latex example > geometry text html latex example > hgu133plus2cdf text html latex > ** building package indices ... > * DONE (hgu133plus2cdf) > > The downloaded packages are in > /tmp/RtmpIMTi6e/downloaded_packages > > Attaching package: 'hgu133plus2cdf' > > > The following object(s) are masked from package:PHYH : > > i2xy > > The following object(s) are masked from package:PHYH : > > xy2i > > AffyBatch object > size of arrays=1164x1164 features (582203 kb) > cdf=HG-U133_Plus_2 (54675 affyids) > number of samples=55 > number of genes=54675 > annotation=hgu133plus2 > > ... it works OK. So should I unpack the hgu133plus2cdf package, > mask out probes (merge into a custom CDF), and then use that? > > Seems like I am missing something obvious here. Need more eyes! > > > Much obliged, thank you in advance for your helpful advice, > > --tim > > -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.