[BioC] Unable to Generate QC Report for mogene10stv1

[James W. MacDonald]

Hi Rick,

On 12/14/2010 3:55 PM, Rick Frausto wrote:
> 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.
> I¹m 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

This indicates that you need more RAM, as you are running out of memory.

> 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]

What exactly is 'mydata', and how did you generate it? The above error 
indicates that you have duplicate row names, which IIRC isn't possible 
to do with an expressionSet.

> 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

More lack of memory errors.


> 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?

First, get more RAM. Second, you will be better off using a 64-bit OS. 
Depending on your hardware, you might be able to just install a 64-bit 
version of R.

Best,

Jim



>
> 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 doesn¹t go to the error, yet, but it¹s 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
>
>
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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