Hi Rick, On 12/17/2010 9:24 PM, Rick Frausto wrote: > Hey Jim, > > Ok, I will give that a go. The only problem is an ExpressionSet contains all > of the necessary information for further analysis (e.g. phenodata, > featuredata and annotation, etc - including, treatment type, cell type, time > points, replicates). I am still learning how to include all of these for a > complete ExpressionSet. As a starting point I've loaded a txt file > containing some of this information (gene abbrev, ontology, probeset ID) > which I created using Affymetrix's Expression Console software, without > replicate, time point and cell type info. Doing this I've gotten as far as > creating a minimal ExpressionSet, which I guess the functions you mention > below do just that but with the information contained in the CEL file only. > > In any case, since as you say, the functions in the online manual create a > proper ExpressionSet why would I get the issue of duplication? Oh yeah, the original question ;-D. Try running QCreport() again, and when it errors out run traceback() and send the output. Also include the output of sessionInfo(). Jim > > In regards to the 64-bit discussion. It may have very well made enough of a > difference as it did not come up with the memory error the last time I tried > it. Going to upgrade to 8GB RAM anyways, can't hurt. > > Cheers, > Rick > > > On 17/12/10 7:20 AM, "James W. MacDonald"<jmacdon at="" med.umich.edu=""> wrote: > >> Hi Rick, >> >> On 12/16/2010 4:13 PM, Rick Frausto wrote: >>> Hi Jim, >>> >>> How do I run an RMA analysis without a proper ExpresionSet? Honest answer, I >>> don't know, I just put in a command line from a manual I found online and it >>> spit out some result- see #3 Affy packages in following link ( >>> http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#biocon_ intro). >> >> You are mistaken. All of the functions mentioned there result in a >> proper ExpressionSet. And if you just do >> >> abatch<- ReadAffy() >> eset<- rma(abatch) >> >> Then you will 100% surely get an ExpressionSet. >> >>> >>> Perhaps you don't need an ExpressionSet until after the preprocessing, at >>> least that is what I get from the "An Introduction to Bioconductor's >>> ExpressionSet Class" written by Seth Falcon, Martin Morgan and Robert >>> Gentleman. Everything seemed to be going smoothly until I tried to get a QC >>> Report. >>> >>> Now, the answer for why I would want to do such a thing is easy. Simply that >>> I don't know any better :) Just started working with R a few days ago, but >>> I'm learning. >>> >>> >>> Apparently Snow Leopard running on 32bit can only utilize about 3.2GB of >>> RAM, whereas 64bit can make use of all 4GB. I'll switch to the 64 bit OS and >>> see if it makes a difference. >> >> Well, it won't be much different. The reason a 32-bit OS can only use >> about 3.2 Gb of RAM is that the OS needs some to run. The 64-bit OS also >> needs to use some RAM, so you won't get all 4 Gb there either. The issue >> is how much RAM can be allocated to a single process, and on a 64-bit OS >> that gets bumped up significantly. >> >> Best, >> >> Jim >> >> >> >>> >>> Thanks for your insight! >>> >>> Cheers, >>> Rick >>> >>> >>> >>> >>> On 16/12/10 11:31 AM, "James W. MacDonald"<jmacdon at="" med.umich.edu=""> wrote: >>> >>>> 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. >>>>>>> I?m 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 >>>>>>> >>> 4,58,59,60,64,65,66,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,9 8,99,102,>> >>>>> >>> 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 doesn?t go to the error, yet, but it?s 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 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at r-project.org >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: >>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>> > -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues