QC in simpleaffy

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Richard Finkers ▴ 20

@richard-finkers-2127

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ADD COMMENT • link updated 17.6 years ago by Crispin Miller ★ 1.1k • written 17.6 years ago by Richard Finkers ▴ 20

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Crispin Miller ★ 1.1k

@crispin-miller-264

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Hi, I fixed this bug yesterday! - The change is in version 2.11.1, which should appear soon. Crispin > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Richard Finkers > Sent: 26 April 2007 07:34 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] QC in simpleaffy > > Hello, > > I tried to do plot an quality control picture for affy data > using the simpleaffy library. To simply illustrate my problem > I used the Dilution dataset available within the bioconductor > package affydata (see below). > I also tried to independently read the values of for example alpha1 > [alpha1 = getAlpha1(cleancdfname(cdfName(Dilution)))] which > resulted in the same error (object : .qcEnv: not found). > Anybody any idea? > > Richard > > > Code & error: > > library(affydata) > > data(Dilution) > > qc(Dilution) > Error in get("spikes", envir = .qcEnv) : object ".qcEnv" not found > > > > sessionInfo() > R version 2.5.0 (2007-04-23) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLA > TE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8 > ;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC > _MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" > "utils" > [7] "datasets" "methods" "base" > > other attached packages: > affydata simpleaffy genefilter survival affy affyio > Biobase > "1.11.2" "2.10.0" "1.14.1" "2.31" "1.14.0" "1.4.0" > "1.14.0" > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

ADD COMMENT • link 17.6 years ago Crispin Miller ★ 1.1k

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Dear list, sorry for this very basic question but I have searched the R manual without success. What function do I need to randomly split a data.frame into two data.frames (for example a data.frame containing 200 rows and 5 columns into two of say 150 and 50 rows each)? Should I first create a vector of 150 random numbers between 1 and 200 (but how?) and then use subset() function? Thanks in advance for your help David

ADD REPLY • link 17.6 years ago kfbargad@ehu.es ▴ 270

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Hi David, This is a general R question and not a Bioconductor-specific question, but... Yes, first create the vector of random numbers using sample(). However, you don't need to use subset() to subset your dataframe, you can just use brackets [] to subset: rand.num <- sample(1:200, 150) sub1.150 <- yourdataframe[rand.num,] sub2.50 <- yourdataframe[-rand.num,] Cheers, Jenny At 07:14 AM 4/26/2007, kfbargad at ehu.es wrote: >Dear list, > >sorry for this very basic question but I have searched the R manual >without success. What function do I need to randomly split a >data.frame into two data.frames (for example a data.frame containing >200 rows and 5 columns into two of say 150 and 50 rows each)? Should I >first create a vector of 150 random numbers between 1 and 200 (but >how?) and then use subset() function? > >Thanks in advance for your help >David > >_______________________________________________ >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 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu

ADD REPLY • link 17.6 years ago Jenny Drnevich ★ 2.2k

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Hi David, kfbargad at ehu.es wrote: > Dear list, > > sorry for this very basic question but I have searched the R manual > without success. What function do I need to randomly split a > data.frame into two data.frames (for example a data.frame containing > 200 rows and 5 columns into two of say 150 and 50 rows each)? Should I > first create a vector of 150 random numbers between 1 and 200 (but > how?) and then use subset() function? Depends on exactly what you want to end up with. To me, splitting implies selecting all rows above row N and all rows below row N-1. N <- sample(1:200, 1) sub1 <- df[1:(N-1),] sub2 <- df[N:200,] or maybe you want to randomly subset rows? idx <- sample(1:200, 150) sub1 <- df[idx,] sub2 <- df[!1:200 %in% idx,] Anyway, time taken to read 'An Introduction to R' would be well spent. Best, Jim > > Thanks in advance for your help > David > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

ADD REPLY • link 17.6 years ago James W. MacDonald 67k

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kfbargad at ehu.es wrote: > Dear list, > > sorry for this very basic question but I have searched the R manual > without success. What function do I need to randomly split a > data.frame into two data.frames (for example a data.frame containing > 200 rows and 5 columns into two of say 150 and 50 rows each)? Should I > first create a vector of 150 random numbers between 1 and 200 (but > how?) and then use subset() function? > See the help for sample(). Sean

ADD REPLY • link 17.6 years ago Sean Davis 21k

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