Dear Dr. Gordon: I saw your reply as below to somebody's question in the BioC mailing list. I already get the password to the list, which is why I can see the list's email, but I still have to wait on the list moderator to review my request for approval and my message is being held because of that. So I copied and pasted my original message send to the list as below and hope you can give me a quick answer or suggestion. Thanks a lot in advance! Hi, List: I have a question regarding paired samples test in limma package. Here is what I got ####W and B are race ####T and N are tumor and normal(paired by same Samples), respectively ####Samples are individual patients: tar$AccNum######## #### > library(limma); > tar<-readTargets("Test_Desc.txt"); > mydata<-read.delim("TestData.txt",as.is=TRUE,row.names=1); > mydata<-mydata[,tar$mRNASampleNames]; > tar$Type<-gsub("Tumor","T",tar$Type) > tar$Type<-gsub("Normal","N",tar$Type) > group1<-paste(tar$RACE,tar$Type,sep="."); > group<-factor(group1, levels=c( "W.T","W.N","B.T","B.N")) > Samples<-factor(tar$AccNum); ####first option to set up the design matrix######### > design<-model.matrix(~Samples+group); > colnames(design)<-sub("group","",colnames(design)); > colnames(design)<-sub("Samples","",colnames(design)); > colnames(design)[1] <- "Intercept"; > con.matrix<-makeContrasts(AA.T_AA.N=B.T-B.N,EA.T_EA.N=-W.N,levels=desi > gn); > lmFit(mydata,design)->fit1; Coefficients not estimable: B.N Warning message: Partial NA coefficients for 26804 probe(s) > contrasts.fit(fit1, con.matrix)->fit2 Error in contrasts.fit(fit1, con.matrix) : trying to take contrast of non-estimable coefficient ################it did not work!!! not sure why??######### ##########then I tried the 2nd option to set up the design matrix#### > design<-model.matrix(~-1+group+Samples); > colnames(design)<-sub("group","",colnames(design)); > colnames(design)<-sub("Samples","",colnames(design)); > con.matrix<-makeContrasts(AA.T_AA.N=B.T-B.N,EA.T_EA.N=W.T-W.N,levels=d > esign); > lmFit(mydata,design)->fit1; Coefficients not estimable: S14810 Warning message: Partial NA coefficients for 26804 probe(s) > contrasts.fit(fit1, con.matrix)->fit2 > eBayes(fit2)->fit3 > #######it works somehow in terms of generating lists, but leave an warning message when I did the fit1 using > lmFit(mydata,design)->fit1 (...Coefficients not estimable: S14810) I am sure why is like this? Using some other dataset, I didn't see such warning at all. It seems dataset specific, I am not sure why there is warning here and whether the list come out is good or not. Could someone please have some suggestions? Thanks in advance! Ming Ming Yi ABCC/ISP National Cancer Institute at Frederick Post Office Box B, Frederick, MD 21702 Phone: 301-846-5764 Fax: 301-846-7070 myi at ncifcrf.gov -----Original Message----- From: Gordon K Smyth [mailto:smyth@wehi.edu.au] Sent: Tuesday, March 29, 2011 6:15 PM To: Zhu, Lihua (Julie) Cc: Wendy Qiao; Bioconductor mailing list Subject: Re: [BioC] average replicate columns in a matrix Dear Julie, Do you mean computing the sum of the replicate columns rather than the mean? You can essentially do that with a call to rowsum() on the transposed matrix. Best wishes Gordon On Tue, 29 Mar 2011, Zhu, Lihua (Julie) wrote: > Dear Gordon, > > Is there a corresponding method for sum over replicate arrays? Thank you so > much for your help! > > Best regards, > > Julie > > > On 3/28/11 6:08 PM, "Gordon K Smyth" <smyth at="" wehi.edu.au=""> wrote: > >> Dear Wendy, >> >> The function avearrays() in the limma package does exactly this: >> >>> library(limma) >>> avearrays(test) >> A B >> [1,] 2.5 10 >> [2,] 3.5 11 >> [3,] 4.5 12 >> >> Best wishes >> Gordon >> >>> Date: Sun, 27 Mar 2011 19:25:29 -0400 >>> From: Wendy Qiao <wendy2.qiao at="" gmail.com=""> >>> To: bioconductor at r-project.org >>> Subject: [BioC] average replicate columns in a matrix >>> Message-ID: >>> >>> I have a matrix like following >>> >>>> test=matrix(c(1:15),nrow=3,ncol=5) >>>> colnames(test)=c("A","A","B","B","B") >>>> test >>> A A B B B >>> [1,] 1 4 7 10 13 >>> [2,] 2 5 8 11 14 >>> [3,] 3 6 9 12 15 >>> >>> I want to calculate the average of each replicates, ie. I want the output to >>> be >>> A B >>> [1,] 2.5 10 >>> [2,] 3.5 11 >>> [3,] 4.5 12 >>> >>> I can do this by looping through each level of the column name, but I was >>> wondering if there is a function for calculating the average of replicates >>> in one step. >>> >>> Thank you in advance. >>> Wendy ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:9}}