[BioC] weird problem with ReadAffy and makecdfenv'd CDF package

[James W. MacDonald]

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


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