[BioC] reduce soychip cel file size

Robert Gentleman rgentlem at jimmy.harvard.edu
Thu Nov 4 23:12:12 CET 2004

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.


> Many thanks,
> Dianjing
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| 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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