Dear All,

I have recently entered the world of R. Through some trial and error I'm
becoming more familiar with R and the relevant Bioconductor Affy packages.
Išm a molecular and cell biologist with rudimentary statistical knowledge
and even less knowledge with respect to R.

When I enter the following:

library(affyQCReport); QCReport(mydata, file="ExampleQC.pdf")

I get some errors in return.

Loading required package: lattice
Error: cannot allocate vector of size 437.4 Mb
In addition: Warning message:
In data.row.names(row.names, rowsi, i) :
  some row.names duplicated:
4,8,9,13,14,15,16,24,25,26,27,28,29,30,31,36,37,38,39,47,48,49,50,51,52,53,5
4,58,59,60,64,65,66,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,102,1
03,104,108,109,110,111,114,119,120,121,122,127,134,136,137,138,139,141,142,1
47,148,149,152,153,156,157,158,159,162,163,164,165,166,167,168,169,170,171,1
73,175,176,179,180,183,184,185,186,191,192,195,197,198,199,200,202,206,207,2
10,219,220,227,228,229,230,233,234,235,240,241,243,245,246,248,249,250,251,2
52,253,257,259,260,266,271,272,276,277,280,281,284,286,287,289,290,291,292,2
96,297,298,302,304,305,306,310,311,312,313,317,318,319,321,322,324,334,337,3
38,339,340,341,345,346,350,351,356,359,362,364,366,367,370,371,373,376,378,3
82,383,384,385,386,387,388,389,391,394,395,397,398,399,400,402,403,405,406,4
07,409,410,411,415,416,418,419,425,431,432,433,434,435,440,441,443,445,447,4
49,450,452,454,455,456,461,464,466,470,472,473,481,487,488,491,492,493,494,4
95,496,497,498,499,501,502,504,506,507,509,511,513,515,516,51 [...
truncated]
R(9062,0xa05c5540) malloc: *** mmap(size=458665984) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(9062,0xa05c5540) malloc: *** mmap(size=458665984) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Error in help(dt[i], package = pkg[i], htmlhelp = TRUE) :
  unused argument(s) (htmlhelp = TRUE)
In addition: Warning messages:
1: In data(package = .packages(all.available = TRUE)) :
  datasets have been moved from package 'base' to package 'datasets'
2: In data(package = .packages(all.available = TRUE)) :
  datasets have been moved from package 'stats' to package 'datasets'
starting httpd help server ... done

Would someone be able to diagnose the problem and suggest a solution?

If it is useful, I am using the following R software: R for Mac OS X GUI
1.35-dev Leopard build 32-bit. If there is any other info that would be
useful please let me know.

I had a read of the AffyQCReport Package pdf and I have added the following
line: QCReport(ReadAffy(widget=TRUE)). Then I tried library(affyQCReport);
QCReport(mydata, file="ExampleQC.pdf") again. It now seems to be doing
something, in other words it doesnšt go to the error, yet, but itšs been
processing for about 10 minutes. I am analyzing 35 chips.

Perhaps it would work if I tried to generate each QCReport page separately
rather than as a whole.

Cordially,
Rick
 
-- 
Rick Frausto
PhD Candidate
The University of Sydney
School of Molecular Bioscience G08
Camperdown, NSW 2006 AUSTRALIA
ricardo.frausto@sydney.edu.au
Phone: 61 2 9036 5354
Lab of Iain L. Campbell






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