Thank you So single threaded Not worry about warnings 64bit R.app installs 64bit stuff Rm'd the old scripts Thank you > From: Kasper Daniel Hansen <khansen at="" stat.berkeley.edu=""> > Date: Mon, 10 Nov 2008 20:30:57 -0800 > To: Loren Engrav <engrav at="" u.washington.edu=""> > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] Does old workspace work? > > On Nov 10, 2008, at 11:50 , Loren Engrav wrote: > >> So I fixed up the old workspace from early 2007 with all your help >> Installed 64bit Intel MacOS stuff >> Installed the new BioC maanova stuff >> Changed one of the 60 chips >> And reran the mixed linear regression previously done in early 2007 >> The command was >> >> ftest.Breed.mix_1000perm081109 <- matest >> (BDeset_gcrma_NoCon25LRmadata.raw.WithAffyID081109, >> BGanova.Br_T.mix081109, >> term = ?Breed?, n.perm = 1000, critical = .9, test.type = c("ftest"), >> shuffle.method = c("sample"), MME.method = c("REML"), test.method = >> c(1,0,1,1), pval.pool = TRUE, verbose = TRUE) >> >> In early 2007 this process took about 40 hours >> This time it took 15 hours which is a serious improvement >> >> Four derivative questions Please >> #1I noticed the computer was using only one of the 8 processors >> Can R/BioC use all of the processors? > > In general R is single threaded, so no. However, on Mac OS, R is > (typically) build against "Altivec" which is an Apple supplied, > multithreaded version of BLAS and Lapack. What this means is that any > computation that involves matrix algebra, will use all your cores. > This could very well be behind the substantial speed up you see. It is > also possible to make packages utilize multiple cores, but this is > somewhat non-standard and hard to do. One example is affypara, for > preprocessing of affy arrays. > >> I received this warning many many times >> 50: In any(parsed.formula$random) ... : coercing argument of type >> 'double' >> to logical >> #2Is this significant? > > I have no idea. > >> I have 64bit R.app but to install the 64bit packages I quit R.app >> and in >> terminal do >> source ("http://www.bioconductor.org/biocLite.R") >> biocLite (c("whatever"), type="source") >> It seems I cannot install the 64bit packages from R.app >> #3Is this true? This has been discussed but I cannot find the >> definitive >> skinny > > If you are using Mac OS X on an Intel machine, the latest Bioconductor > builds includes 64bit versions. So that means that type = "mac.binary" > should give you a 64 bit version. > > Whether or not you do this from R.app should not have any impact. > >> In the old workspace there are several objects like >> "biocinstall.defaultPkgs" >> "biocinstall.graphPkgs" >> "biocinstall.litePkgs" >> which are scripts of various types I guess to install groups of >> packages, >> like >> >> function() >> { >> contriburl = "http://bioconductor.org/packages/1.9/bioc/src/contrib >> " >> available.packages(contriburl)[, "Package"] >> } >> >> #4Are these scripts old and no longer used to install groups? > > These scripts are by-product of doing > R> source(http://www.bioconductor.org/biocLite.R") > and can safely be deleted. They will be recreated, if necessary, > everytime you source biocLite. > > Kasper > >> Thank you again >> >>> From: Loren Engrav <engrav at="" u.washington.edu=""> >>> Date: Fri, 31 Oct 2008 15:38:12 -0700 >>> To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>> Subject: Re: [BioC] Does old workspace work? >>> >>> Cool, I can deal with evolution >>> >>> And the archives will be a super addition to ? and google, thank >>> you, maybe >>> better than google >>> >>> So we biopsied shallow and deep wounds on 3 Duroc pigs and 3 >>> Yorkshire pigs >>> at 1 2 3 12 and 20 weeks, this then is 60 porcine chips with 24123 >>> probe >>> sets on the chip, we were interested in chip2-chip1, chip4-chip3, etc >>> And studied the differences with R/maanova and various biologic data >>> reduction steps to achieve a group of 1289 for further study >>> >>> So for the fun of it, I compared chip2-chip1 in gcrmaOld and >>> gcrmaNew >>> >>> In gcrmaOld there were no differences of exactly zero >>> In gcrmaNew 249/24123 were exactly zero which seems kinda funny >>> This affected 4 in the group of 1289 but did not change anything >>> >>> 9247/24123 differences changed sign which is potentially bad for >>> this study; >>> but after cutting those with log ratio < .5 as too trivial to worry >>> about in >>> this complex system, zero were left >>> >>> I could rerun this, but given this, and that the old Mac PRO PPC >>> took ~40 >>> hours to run the mixed linear regression, I think the old data is >>> just fine >>> >>> And since >>> objNew <- as(objOld, "ExpressionSet") works would appear I am back in >>> business >>> >>> Thank you all >>> >>> >>> From: Sean Davis <sdavis2 at="" mail.nih.gov=""> >>> Date: Fri, 31 Oct 2008 15:00:47 -0400 >>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>> Subject: Re: [BioC] Does old workspace work? >>> >>> >>> >>> On Fri, Oct 31, 2008 at 2:47 PM, Loren Engrav <engrav at="" u.washington.edu="">>>> >>> wrote: >>>> Thank you, got it >>>> >>>> exprs(obj) is missing from the output but shows in ?ExpressionSet >>>> and puts >>>> up the data so I can see it >>>> >>>> And now perhaps one final question to understanding this old data >>>> and >>>> progress >>>> >>>> Long long ago I did >>>> AA_ReadAffy <- ReadAffy() >>>> ABeset_gcrma < gcrma (AA_ReadAffy) >>>> >>>> Now I do >>>> AA_ReadAffy081031 <- ReadAffy() #on the same .cel files >>>> ABeset_gcrma081031 <- gcrma (AA_ReadAffy081031) >>>> >>>> Then I do >>>> Show(ABeset_gcrma) and exprs(ABeset_gcrma081031) >>>> >>>> And they do not match, for example >>>> Probe set Ssc.10026.1.A1_at >>>> ABeset_gcrma is 4.124689 >>>> ABeset_gcrma081031 is 3.344443 >>>> >>>> ReadAffy changed? >>>> gcrma changed? >>> >>> See: >>> >>> http://thread.gmane.org/gmane.science.biology.informatics.conducto r/16664/fo >>> cus=16664 >>> >>> The bioconductor archive is your friend. >>> >>> Sean >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >