[BioC] reduce soychip cel file size

Holger Schwender holger.schw at gmx.de
Fri Nov 5 11:17:10 CET 2004

Hi Dianjing,

I also do not think that the problem is the size of the chip since we have
applied rma to a set of about 20 X3p chips which also contain more than
60,000 probe sets. And it perfectly worked on a computer with 2 GB RAM.
Using just.rma it even worked on a 512 MB RAM machine.

If you are however really interested in using just a subset of the probe
sets, it will be possible to make your own cdf environment with altcdfenvs,
then tell R that your AffyBatch object has this cdfName and  then apply rma
only to the probe sets in your alternative cdf environment. Please let me
know if you are interested in a function that makes such an alternative cdf
environment since I have written a couple of such functions for one of my
collegues who was interested in using just some of the probe sets.


> On Thu, Nov 04, 2004 at 02:08:09PM -0500, Dianjing Guo wrote:
> > We constantly experienced problems with rma function with soybean chip. 
> > Since the possible reason being the chip is too huge, i wonder whether 
> > there's a way to reduce the cel file size by taking only part of the raw
> > intensity info for normalization. Any one can comment /addvise on that?
>   That does not seem like a very good idea. I have not seen any
>   postings that suggest that size is the issue; have you made them? 
>   None of this needs to be mysterious in any way. 
>   You should 1) make sure you have an up to date R, and an up to date
>   version of the package. If you get errors, such as segmentation
>   faults then you can use 
>    R -d gdb 
>   provided you have compiled R with the -g option (and if not then you
>   will need to recompile it). From there you can track down the source
>   of the bug and it can be fixed.
>   For other bugs (such as problems in R code) there are options such
>   as using debug etc. 
>   It is generally much better to figure out what is wrong, and why
>   than to invent rather peculiar one-off solutions.
>   Robert
> > 
> > Many thanks,
> > Dianjing
> > 
> > _______________________________________________
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> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> -- 
> | Robert Gentleman                 phone : (617) 632-5250                 
>  |
> | Associate Professor              fax:   (617)  632-2444                 
>  |
> | Department of Biostatistics      office: M1B20                          
>  |
> | Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu      
>  |
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