[BioC] Re: Bioconductor Digest, Vol 2, Issue 32

[Michael McDonald]

hi derek,

I have a 400mHz G4, with X 10.2.5 and am using Jan de Leeuw's 
precompiled R package at http://gifi.stat.ucla.edu/pub/.  All you would 
need is the MacOsX developer tools and X11 from apple, you could also 
install fink if you want.  I was getting errors like yours(with 1.6.2) 
and I recall it had to do with the cdf file not being installed, it is 
available from the bioconductor website and can be installed from your 
root directory using : sudo R CMD INSTALL "path to the cdf file".

I am new to the list and I have also seen the error messages when 
trying to read in cel files, and when using normalize.loess as 
described in paul boutros email.  I did install the affy developer 
package, along with the devel packages of tkWidgets and Biobase, 
everything seems to be fine for now, except that the loess 
normalization gives a memory error for the size of the matrix?:
Done with 1 vs 2  in iteration  1
Done with 1 vs 3  in iteration  1
Done with 2 vs 3  in iteration  1
1 0.001657622
Warning messages:
1: k-d tree limited by memory. ncmax= 5002
2: k-d tree limited by memory. ncmax= 5002
3: k-d tree limited by memory. ncmax= 5002

Does anyone have suggestions on how to increase the size of ncmax?

Best,
mike


>
> Message: 5
> Date: Mon, 28 Apr 2003 14:00:37 -0700
> From: "Stirewalt, Derek L" <dstirewa at fhcrc.org>
> Subject: [BioC] MAC INSTALLATION AFFY PACKAGE
> To: "'bioconductor at stat.math.ethz.ch'"
> 	<bioconductor at stat.math.ethz.ch>
> Message-ID: <B1C5649A402DD51190930002B330A181014388AF at shemp.fhcrc.org>
> Content-Type: text/plain;	charset="iso-8859-1"
>
> HI,
> WE ARE TRYING TO INSTALL AFFY PACKAGE AND BIOC ON A IMAC WITH OS10 AND 
> WHEN
> WE TRY TO READ A CEL FILE HERE IS WHAT WE GET:
>
>
>> library(affy)
> Welcome to Bioconductor
> 	 To view some introductory material -- look at our vignettes
> 	 Simply type: openVignette()
> 	 to see the available vignettes
> 	 To read a vignette see the openVignette help page for details
> Creating a new generic function for "summary" in package
> Biobase
>
> Attaching package `Biobase':
>
>
> 	The following object(s) are masked from package:base :
>
> 	 split summary
>
>
> Attaching package `affy':
>
>
> 	The following object(s) are masked from package:base :
>
> 	 barplot boxplot colnames hist history image ncol nrow
>
>> Data <- ReadAffy()
> Error in getInfoInAffyFile(filename, "CEL", "HEADER", "DatHeader", 
> compress =
> compress) :
> 	Cannot open the file Wilson:Applications:rm162::0126192.CEL.
> SO IT SEEMS THAT BIOC IS ABLE TO GET AFFY WORKING BUT READNG THE CEL 
> FILE
> SEEMS T BE A TROUBLE. WE ARE RUNNING BIOC on R1.6.2 and the Affy 
> package is
> the routine one, not the developmental package.
> ANY HELP WELCOME ! THANKS
>
> Derek L. Stirewalt, MD
> Associate in Clinical Research
> D4-100, FHCRC
> 1100 Fairview Ave N
> Seattle, WA  98109
> (206)-667-5113
>
--------------------------------------------------
Michael J. McDonald  Ph.D.	
Univesite of Geneve c/o Duboule Lab
Department of Zoologie and Biologie Animale
Quai Ernest-Ansermet 30
CH-1211 Geneve 4
phone 41.22.702.67.94