[BioC] just.gcrma and gcrma

James MacDonald jmacdon at med.umich.edu
Thu Apr 22 17:40:17 CEST 2004


That's a bug in just.gcrma. I am going to commit the bugfix to BioC
momentarily, but it will take a while to propagate to the BioC website.
In the interim, you can source the attached file before running
just.gcrma().

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Oosting, J. (PATH)" <J.Oosting at lumc.nl> 04/22/04 08:04AM >>>
I have downloaded the Michigan Lung cancer dataset celfiles from the 
CAMDA
2003 Conference Contest Datasets, for testing a survival analysis. (
http://www.camda.duke.edu/camda03/datasets/ )

When I tried to perform gcrma(), I got into memory problems so I tried
just.gcrma(), but this caused the following error:
Computing affinities..Done.
Adjusting for optical
effect......................................................................
...........................Done.
Adjusting for non-specific binding.Error in quantile.default(y, Q) :
Missing
values and NaN's not allowed if `na.rm' is FALSE

This same error appears when performing this on much smaller subsets,
with
which gcrma() has no problem

Used Versions
Windows 2000
R 1.9
gcrma 1.0.6

Jan

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