Question: SAM analysis of two color microarray data
5.1 years ago by
Guest User • 12k
Guest User • 12k 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. 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.
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