[BioC] Unable to Generate QC Report for mogene10stv1

Thu Dec 16 20:31:20 CET 2010

Hi Rick,

On 12/16/2010 12:57 PM, Rick Frausto wrote:
> Thanks Jim! How much memory would I need, I currently have 4GB, but have
> quite a few other programs running in the background...I'll see if closing
> them helps. Perhaps setting up an "ExpressionSet" would solve the problem. I
> just started reading up on how to set one of these up yesterday. Will do
> this and see if the duplicates will go away.
>
> The "mydata" originates from CEL files and then I run the RMA analysis on
> it, but I didn't actually set up a proper ExpressionSet. I'm guessing that
> doing this might reduce the QCReport PDF file size quite considerably since
> I won't have any duplication and will make further analysis easier.

How do you run an RMA analysis without setting up a proper 
ExpressionSet? The default behavior is to create one. In addition, why 
would you want to do such a thing? The ExpressionSet class is 
specifically designed to contain these sorts of data.

>
> I'm running Snow Leopard OSX which can be set up as 64bit. Would running as
> 64bit still necessitate more RAM?

Probably. The difference isn't efficiency, but the ability to address 
more RAM. A 32-bit OS can still address all the available memory that 
you will have with just 4 Gb RAM, so you need to bump that up if you 
want to do all the chips together. As for how much, I don't know. Since 
RAM isn't that expensive these days, you might look at maxing your box out.

Best,

Jim

>
> Thanks again,
> Rick
>
>
> On 15/12/10 7:45 AM, "James W. MacDonald"<jmacdon at med.umich.edu>  wrote:
>
>> 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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