[BioC] gcrma and combineAffyBatch

[Michael Palumbo]

jim,

thanks much for the response. well, a definitive answer, even if it's 
not the one you're looking for, is better than a vague answer or no 
answer at all. given what appears to be a good deal of work involved in 
going the gcrma() route, with no guarantee of success, it seems pretty 
clear that using rma() is the way to go.

in fact, i just ran rma() on an affy batch object returned by 
combineAffyBatch() that contains data from 40 chips - 25 from mouse 430a 
and 15 from mouse 430_2, and it ran without error. i'm happy.

thanks again,
mike


Michael Palumbo					palumbo at wadsworth.org
Bioinformatics Core			 TGI/RTP & VM: (518) 880-1360
Wadsworth Center			          CMS: (518) 402-4587
Center for Medical Science
New York State Dept of Health
150 New Scotland Ave
Albany, NY 12208



James W. MacDonald wrote:
> Hi Michael,
>
> Michael Palumbo wrote:
>> hello,
>>
>> i'm new to bioconductor and processing array data, but i'm not new to 
>> R - not an expert, either, let's say mildly competent...
>>
>> (output of sessionInfo() is at bottom of this email.)
>>
>> the short version of my question:
>> i'm having trouble running gcrma() on an affy batch object returned 
>> from combineAffyBatch(). the combined object is created by combining 
>> data from two types of mouse chips: moe430a and mouse4302. gcrma() 
>> returns this error:
>>
>>  > gcrma.eset.A.V2 <- gcrma(comb.A.V2$dat)
>>
>>  Adjusting for optical effect...Done.
>>
>>  Computing affinitiesError in getCDF(cdfpackagename) : The current 
>> operation could not  access the Bioconductor repository. Please check 
>> your internet connection, and report  further problems to 
>> bioconductor at stat.math.ethz.ch
>>
>>
>> the long version of my question, and more code:
>> i believe the combining of chip data occurs without error. i put the 
>> newly computed cdf in the global environment - i think this is where 
>> the problem is - like it's not being recognized.
>
> So there are two problems here. First, getCDF() looks for an 
> _installed_ cdf package, rather than an environment, and if it doesn't 
> find the installed package it tries to get one from BioC, which as you 
> know is failing. I could envision some sort of hackery that could get 
> around this problem. However...
>
> The second problem is that you don't have a probe package that 
> corresponds to the cdf you are using. Without the probe package you 
> will not be able to proceed anyway, so the first point is sorta moot.
>
> If you are really wedded to the idea of using gcrma(), I suppose you 
> could get the probe_tab files for each of the chips you are using 
> (from the Affy website), use awk or Perl or some such to come up with 
> a combined probe_tab file that would correspond to the combined cdf 
> that you are using, build the probe package, do some hack to getCDF() 
> to find the cdfenv and then proceed happily.
>
> Or else you could forget all that stuff, do RMA on your data, and 
> proceed (slightly less) happily, but without spending all the time 
> required to do the above.
>
> Unless there is some obvious solution that escapes me. There are 
> others here who use gcrma() all the time who may have already met and 
> surmounted this problem. Although, as you noted, nobody is talking 
> about it ;-D.
>
> Sorry I can't be more helpful...
>
> Best,
>
> Jim
>
>
>>
>>
>>> library(mouse4302cdf)  
>>
>>
>>> library(moe430acdf)
>>
>>
>>> comb.A.V2 <- combineAffyBatch(list(A,V2),c("moe430aprobe",
>>
>>   "mouse4302probe"),newcdf="comb.430a.4302.cdf")
>>
>>  package:moe430aprobe    moe430aprobe   
>>  package:mouse4302probe  mouse4302probe 
>>  245487 unique probes in common
>>
>> # put new cdf in global environment
>>
>>
>>> comb.430a.4302.cdf <- comb.A.V2$cdf
>>
>>
>>> library(gcrma)
>>
>>
>>   Loading required package: splines
>>
>>
>>> gcrma.eset.A.V2.3 <- gcrma(comb.A.V2$dat)
>>
>>
>>   Adjusting for optical effect...Done.
>>
>>   Computing affinitiesError in getCDF(cdfpackagename) : The current 
>> operation could not   access the Bioconductor repository. Please 
>> check your internet connection, and report   further problems to 
>> bioconductor at stat.math.ethz.ch
>>
>> ------
>> when i check the cdf of the combined object, it looks correct to me:
>>
>>
>>
>>> cdfName(comb.A.V2$dat)
>>
>>
>> [1] "comb.430a.4302.cdf"
>>
>>
>> --------------------
>>
>>  > sessionInfo()
>> R version 2.4.1 (2006-12-18)
>> i386-pc-solaris2.10
>>
>> locale:
>> /en_US.ISO8859-1/C/C/en_US.ISO8859-1/en_US.ISO8859-1/C
>>
>> attached base packages:
>> [1] "splines"   "tools"     "stats"     "graphics"  "grDevices" 
>> "utils"   [7] "datasets"  "methods"   "base"   
>> other attached packages:
>>  hgu95av2probe    hgu95av2cdf      hgu95acdf mouse4302probe   
>> moe430aprobe
>>          "1.0"        "1.4.3"        "1.4.1"       "1.14.0"       
>> "1.14.0"
>>          gcrma     moe430acdf   mouse4302cdf    matchprobes           
>> affy
>>        "2.6.0"       "1.14.0"       "1.14.0"        "1.6.0"       
>> "1.12.2"
>>         affyio        Biobase
>>        "1.2.0"       "1.12.2"
>>
>> i've searched the email list (what i think is) extensively and 
>> although i've found other mentions of similar problems i haven't 
>> stumbled across a solution that works for me. in particular, i tried 
>> a fairly different approach that involved creating affinity info 
>> objects and that didn't work either (i can supply the error of that 
>> attempt if necessary). the method i tried is described here 
>> <http://thread.gmane.org/gmane.science.biology.informatics.conductor/2500/focus=2747>. 
>>
>>
>> thanks in advance for any and all help,
>> mike
>>
>
>