Hai, I just want to know the model that we have to use for the LIMMA package for analysing the agilent single colour data. Currently am using the model: *design <- model.matrix(~ 0+factor(c(1,1,2,2)))* *colnames(design) <- c("group1", "group2")* *fit <- lmFit(y.ave, design)* *print(design) * Is this model design suits for analyzing the Agilent single color data using the LIMMA package without having any replicates? Instead of using the replicate of the samples we have just used the pooled samples in analyzing the data. -- [[alternative HTML version deleted]]

Hello, As far as i know, the groups in LIMMA for samples are not always down to the fact if they are replicates or not. You label samples as, in this case, 1 or 2 depending on treatment or a condition (such as duration of treatment, cell lines etc). For example if you have 2 samples treated with DMSO and 2 treated with CPI, the design matrix can be of the type design <-model.matrix(~0+factor(c(1, 1, 2, 2). If you have 2 DMSO samples coming from same cell line having 1 replicate each then the design matrix can be design <-model.matrix(~0+factor(c(1,-1,1,-1) Hope this helps. Ekta -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Muralidharan V Sent: 27 April 2012 11:46 To: bioconductor at r-project.org Subject: [BioC] Model matrix used in analysis of Agilent single color data Hai, I just want to know the model that we have to use for the LIMMA package for analysing the agilent single colour data. Currently am using the model: *design <- model.matrix(~ 0+factor(c(1,1,2,2)))* *colnames(design) <- c("group1", "group2")* *fit <- lmFit(y.ave, design)* *print(design) * Is this model design suits for analyzing the Agilent single color data using the LIMMA package without having any replicates? Instead of using the replicate of the samples we have just used the pooled samples in analyzing the data. -- [[alternative HTML version deleted]] _______________________________________________ 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 The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com