Dear Biconductor, I am new to analysis of micro array data and I am trying to analyse a two colour micro array data. I was trying to reproduce the results in the paper (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-120/ ). In this paper, the authors say that they have normalized the data using 1. print tip loess method and 2. performed analysis using SAM. 1. From limma package userguide, I understand that we cannot perform print tip loess normalization on Agilent arrays, therefore, I have performed loess normalization. Currently, I have run following code in R targets <- readTargets("Psamples.txt") # Psamples contains the file list from raw data. RG <- read.maimages(targets, source="agilent") RGb0 <- backgroundCorrect(RG, method="none") MA0 <- normalizeWithinArrays(RGb0, method="loess") #Normalization using loess method 2. I have found that the siggenes can be used to perform SAM analysis on array express data. The sam function requires data in the form of matrix/data frame or expressionset object. The second input required by sam is cl which is class labels. I have used following command to perform SAM analysis sam.analyse = sam(MA0$M,MA0$genes$ControlType) as according to my understanding MA0$M contains the normalized data and MA0$genes$ControlType contains the class labels. But I am getting the error: The length of cl must be equal to the number of columns of data. I am not sure how to correct it. Please can you confirm how can I use data to perform the analyses. Is there anything I am doing wrong? Regards, -- output of sessionInfo(): targets <- readTargets("Psamples.txt") # Psamples contains the file list from raw data. > RG <- read.maimages(targets, source="agilent") Read 251486817346_1.txt Read 251486817346_2.txt Read 251486817346_3.txt Read 251486817346_4.txt > RGb0 <- backgroundCorrect(RG, method="none") > MA0 <- normalizeWithinArrays(RGb0, method="loess") > sam.analyse = sam(MA0$M,MA0$genes$ControlType) Error in adjust.for.mt(data, cl, var.equal = var.equal) : The length of cl must be equal to the number of columns of data. -- Sent via the guest posting facility at bioconductor.org.

On Thu, Sep 4, 2014 at 12:29 PM, Shan-e-Ahmed Raza [guest] < guest at bioconductor.org> wrote: > Dear Biconductor, > > I am new to analysis of micro array data and I am trying to analyse a two > colour micro array data. > I was trying to reproduce the results in the paper ( > http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-120/ ). In this > paper, the authors say that they have normalized the data using 1. print > tip loess method and 2. performed analysis using SAM. > > 1. From limma package userguide, I understand that we cannot perform > print tip loess normalization on Agilent arrays, therefore, I have > performed loess normalization. > > Currently, I have run following code in R > > targets <- readTargets("Psamples.txt") # Psamples contains the file list > from raw data. > RG <- read.maimages(targets, source="agilent") > RGb0 <- backgroundCorrect(RG, method="none") > MA0 <- normalizeWithinArrays(RGb0, method="loess") #Normalization using > loess method > > 2. I have found that the siggenes can be used to perform SAM analysis > on array express data. The sam function requires data in the form of > matrix/data frame or expressionset object. The second input required by sam > is cl which is class labels. > > I have used following command to perform SAM analysis > > sam.analyse = sam(MA0$M,MA0$genes$ControlType) > > as according to my understanding MA0$M contains the normalized data and > MA0$genes$ControlType contains the class labels. > But I am getting the error: The length of cl must be equal to the number > of columns of data. I am not sure how to correct it. > The first step is to make sure that your understanding is actually correct. What do you get from MA0$genes$ControlType and ncol(MA0$M) Best, Jim > > Please can you confirm how can I use data to perform the analyses. Is > there anything I am doing wrong? > > Regards, > > > -- output of sessionInfo(): > > targets <- readTargets("Psamples.txt") # Psamples contains the file list > from raw data. > > RG <- read.maimages(targets, source="agilent") > Read 251486817346_1.txt > Read 251486817346_2.txt > Read 251486817346_3.txt > Read 251486817346_4.txt > > RGb0 <- backgroundCorrect(RG, method="none") > > MA0 <- normalizeWithinArrays(RGb0, method="loess") > > sam.analyse = sam(MA0$M,MA0$genes$ControlType) > Error in adjust.for.mt(data, cl, var.equal = var.equal) : > The length of cl must be equal to the number of columns of data. > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]]