Hi, I've a problem using limma with bluefuse output files (I've saved those files as .xls) I'm able to use one file per time without any trouble but when I try to load more than one file using a "target" file, I receive an error message. I've installed R 2.3.1 and limma 2.7.3 Sample session below: #Using right package! >library(limma) #I create an object as a target from file > target<-readTargets(file="targets.txt",path="C:\\Playground\\Micro") #This is the object > target SlideNumber Name FileName Cy3 Cy5 array1 1 c1 array1.xls control treatment array2 2 c2 array2.xls control treatment #and how I use the read.maimage > RG<-read.maimages(target$FileName,source="bluefuse",path="C:\\Playgr ound\\Micro") Read C:\Playground\Micro/array1.xls Error in switch(source2, quantarray = { : could not find function "readBlueFuseHeader" #I've also tried to use a vector with file names instead of a target object, #but the result happen to be the same. > files<-c("array1.xls","array2.xls") > RG<-read.maimages(files,source="bluefuse",path="C:\\Playground\\Micr o") Read C:\Playground\Micro/array1.xls Error in switch(source2, quantarray = { : could not find function "readBlueFuseHeader" #I've not found any information about readBlueFuseHeader in the documentation (i'm using ver. 2.7.3) #If I call the function I receive the same error! > readBlueFuseHeader() Error: could not find function "readBlueFuseHeader" I'm a new user of R, please let me know what I'm doing wrong. Kind Regards Alessio

Hi, There is an error with the limma code for using read.maimages with bluefuse. I've informed the author (Gordon Smyth) and a fix will be included in the next release of limma. In the meantime if you'd like my edited version of read.maimages that works with bluefuse data please email me and I'll send it to you. Mike Smith On 20 Jun 2006 at 17:51, Alessio Venier wrote: > Hi, > > I've a problem using limma with bluefuse output files (I've saved those files as .xls) > I'm able to use one file per time without any trouble but when I try to load more than > one file using a "target" file, I receive an error message. > I've installed R 2.3.1 and limma 2.7.3 > > Sample session below: > > #Using right package! > >library(limma) > > #I create an object as a target from file > > target<- readTargets(file="targets.txt",path="C:\\Playground\\Micro") > > #This is the object > > target > SlideNumber Name FileName Cy3 Cy5 > array1 1 c1 array1.xls control treatment > array2 2 c2 array2.xls control treatment > > #and how I use the read.maimage > > RG<- read.maimages(target$FileName,source="bluefuse",path="C:\\Playg round\\Micro") > Read C:\Playground\Micro/array1.xls > Error in switch(source2, quantarray = { : could not find function "readBlueFuseHeader" > > #I've also tried to use a vector with file names instead of a target object, > #but the result happen to be the same. > > > files<-c("array1.xls","array2.xls") > > RG<- read.maimages(files,source="bluefuse",path="C:\\Playground\\Micro ") > Read C:\Playground\Micro/array1.xls > Error in switch(source2, quantarray = { : could not find function "readBlueFuseHeader" > > #I've not found any information about readBlueFuseHeader in the documentation (i'm using ver. 2.7.3) > #If I call the function I receive the same error! > > > readBlueFuseHeader() > Error: could not find function "readBlueFuseHeader" > > I'm a new user of R, please let me know what I'm doing wrong. > > Kind Regards > > Alessio > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Group Hutchison / MRC Research Centre Department of Oncology University of Cambridge Hills Rd, Cambridge CB2 2XZ Email: mls40 at cam.ac.uk