Question: Treatment vs. Control in cDNA Dye Swap Experiment
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gravatar for White, Charles E WRAIR-Wash DC
16.5 years ago by
I'm trying to use maTwoSamples but I don't understand the parameters. Assistance would be appreciated. Using the example swirl data, I'm doing the following: {rm(list=ls(all=TRUE))} > library(marrayInput) > swirl.layout <- read.marrayLayout(fname = "fish.gal", ngr = 4, ngc = 4, nsr = 22, + nsc = 24, skip = 21,ctl.col = 4) > ctl <- rep("Control", maNspots(swirl.layout)) > ctl[maControls(swirl.layout) != "control"] <- "N" > maControls(swirl.layout) <- factor(ctl) > swirl.targets <- read.marrayInfo("SwirlSample.txt") > swirl.gnames <- read.marrayInfo("fish.gal",info.id = 4:5, labels = 5, skip = 21) > datadir <- getwd() > fnames <- dir(path=datadir,pattern=paste("*", "spot", sep="\.")) > swirl<- read.Spot(fnames, path=datadir, + layout = swirl.layout, + gnames = swirl.gnames, + targets = swirl.targets) [1] "Reading c:\\...\\Demo/swirl.1.spot" [1] "Reading c:\\...\\Demo/swirl.2.spot" [1] "Reading c:\\...\\Demo/swirl.3.spot" [1] "Reading c:\\...\\Demo/swirl.4.spot" > library(marrayNorm) > swirl.norm <- maNormMain(swirl) > swirl.targets Object of class marrayInfo. maLabels # of slide Names experiment Cy3 experiment Cy5 date 1 81 81 swirl.1.spot swirl wild type 2001/9/20 2 82 82 swirl.2.spot wild type swirl 2001/9/20 3 93 93 swirl.3.spot swirl wild type 2001/11/8 4 94 94 swirl.4.spot wild type swirl 2001/11/8 comments 1 NA 2 NA 3 NA 4 NA Number of labels: 4 Dimensions of maInfo matrix: 4 rows by 6 columns Notes: SwirlSample.txt > # swap dye posiions > library(marrayTools) > maTwoSamples(targetfile=swirl.targets, normdata=swirl.norm, Trt='swirl', Ctl='wild type', targetID = 3, slidesID = 2, dyesID = 4, RedID = 5, path = ".", output = TRUE) Error in readLines(con, n, ok) : `con' is not a connection Error in maInfo(read.marrayInfo(targetfile)) : Unable to find the argument "object" in selecting a method for function "maInfo" > Charles E. White, Biostatistician Walter Reed Army Institute of Research 503 Robert Grant Ave., Room 1w102 Silver Spring, MD 20910-1557 301 319-9781 WRAIR Home Page: http://wrair-www.army.mil/
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ADD COMMENTlink modified 16.5 years ago by Jean Yee Hwa Yang920 • written 16.5 years ago by White, Charles E WRAIR-Wash DC70
Answer: Treatment vs. Control in cDNA Dye Swap Experiment
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gravatar for Jean Yee Hwa Yang
16.5 years ago by
Jean Yee Hwa Yang920 wrote:
Hi Charles, maTwoSamples were design to swap cDNA Dye Swap Experiment from target files coming from data bases with one one channel information per line. In the swirl example, it will be looking for the following input E.g. TargetName Slides Dyes PrintDate Names swirl slide81 3 2001/9/20 swirl.1.spot wildtype slide81 5 2001/9/20 swirl.1.spot swirl slide82 5 2001/9/20 swirl.2.spot I will update the documents and make this clearer. For the mean time to calculate various statistics from dye swap experiment, you will need to specified the dye flip manually. There are two alternative options: A) ## Normalized and extra your data M <- maM(manorm(swirl)) ## Swap the Dye manually swirl.M <- sweep(M, 2, c(-1, 1, -1, 1), FUN="*") ## Calculate the various statistics using widget (option (a)) ## Select from the widget the statistics you like to calculate, widget.Stat(swirl.M, outputName="myres") ## or use maStat, here you can write your own functions in addition to the ## mean, t-stat and B-stat that is provided (option (b)). res <- maStat(X, funNames=c("meanFun", "ttestFun")) ## use stat.gnames to select the top genes. stat.gnames(res[,"meanFun"], maGeneTable(swirl), crit=30) B) Use the package limma library(limma) M <- maM(maNorm(swirl)) design <- c(-1,1,-1,1) ## Fit a linear model fit <- lm.series(M, design) ## t-stat can be obtain from fit$coef ## B-stat (empirical Bayes) eb <- ebayes(fit) ## Generate 30 top genes using toptable(number=30, genelist=maGeneTable(swirl), fit=fit, eb=eb) Hope this help. Cheers Jean On Fri, 30 May 2003, White, Charles E WRAIR-Wash DC wrote: > I'm trying to use maTwoSamples but I don't understand the parameters. > Assistance would be appreciated. Using the example swirl data, I'm doing the > following: > > > maLabels # of slide Names experiment Cy3 experiment Cy5 date > 1 81 81 swirl.1.spot swirl wild type 2001/9/20 > 2 82 82 swirl.2.spot wild type swirl 2001/9/20 > 3 93 93 swirl.3.spot swirl wild type 2001/11/8 > 4 94 94 swirl.4.spot wild type swirl 2001/11/8 > comments > 1 NA > 2 NA > 3 NA > 4 NA >
ADD COMMENTlink written 16.5 years ago by Jean Yee Hwa Yang920
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