I've been trying with no success to analyze 2-channel array data from ArrayExpress. The scanner specific data files are not available (I've used ImaGene files previously with ease.) I used the ArrayExpress package to get the data very conveniently and easily. The data are loaded into R as NChannelSet data. I cannot sort out how to get this into a format acceptable by limma. It's easy enough to access the channels as well as annotations but limma methods such as (for example) limma's normalizeWithinArrays() normalizeWithinArrays(object, layout, method="printtiploess", weights=object$weights, span=0.3, iterations=4, controlspots=NULL, df=5, robust="M", bc.method="subtract", offset=0) where object: object of class 'list', 'RGList' or 'MAList' containing red and green intensities constituting two-color microarray data. > ae = ArrayExpress("E-FPMI-11", rawcol=list(R="Software Unknown:Signal Mean_cy5", G="Software Unknown:Signal Mean_cy3", Rb="Software Unknown:Background Mean_cy5", Gb="Software Unknown:Background Mean_cy3")); > class( ae ) [1] "NChannelSet" attr(,"package") [1] "Biobase" > test = normalizeWithinArrays( ae ) Error in MA.RG(object, bc.method = bc.method, offset = offset) : Object doesn't contain R and G components I also notice that the convert routines will convert to NChannelSet but not from NChannelSet to other types such as used by limma (RGList, MAList). I am tempted to now write the data back to file and construct a generic 2-color data object using limma::read.maimages(). But this seems an odd thing to do. I've also tried getting the data directly to file and then using the RMAGEML package but it seems to not install due to need for SJava installed which won't install on either Mac (my workstation) or Linux Ubuntu 7.10 due to compilation errors in the SJava C code (subject of another post if needed). How do I use NChannelSet data or convert to RGList or MAList? Thanks for any help... -- ------------------------------------------------- Christopher Fjell, PhD Centre for Microbial Diseases and Immunity Research Department of Microbiology and Immunology University of British Columbia 2259 Lower Mall Vancouver, British Columbia, Canada, V6T 1Z4 cfjell at interchange.ubc.ca / chris at cmdr.ubc.ca

Hi Chris -- Chris Fjell wrote: > I've been trying with no success to analyze 2-channel array data from > ArrayExpress. The scanner specific data files are not available (I've > used ImaGene files previously with ease.) > > I used the ArrayExpress package to get the data very conveniently and > easily. The data are loaded into R as NChannelSet data. > > I cannot sort out how to get this into a format acceptable by limma. > It's easy enough to access the channels as well as annotations but limma > methods such as (for example) limma's normalizeWithinArrays() > > normalizeWithinArrays(object, layout, method="printtiploess", > weights=object$weights, span=0.3, iterations=4, controlspots=NULL, df=5, > robust="M", bc.method="subtract", offset=0) > > where > > object: object of class 'list', 'RGList' or 'MAList' containing red > and green intensities constituting two-color microarray data. > >> ae = ArrayExpress("E-FPMI-11", rawcol=list(R="Software Unknown:Signal > Mean_cy5", G="Software Unknown:Signal Mean_cy3", Rb="Software > Unknown:Background Mean_cy5", Gb="Software Unknown:Background Mean_cy3")); I looked at ?"RGList-class" and tried rg <- new("RGList", as.list(assayData(ae))) ma <- normalizeWithinArrays(rg, method="median") I could have moved more info. into the RGList with args <- c(as.list(assayData(ae)), list(targets=pData(ae), genes=fData(ae))) rg <- new("RGList", args) If I wanted to use some normalization methods, e.g., loess, then I'd need to extract the relevant information from fData(ae), and feed this to the 'layout' argument of ?normalizeWithinArrays. Does that get you on your way? Martin >> class( ae ) > [1] "NChannelSet" > attr(,"package") > [1] "Biobase" >> test = normalizeWithinArrays( ae ) > Error in MA.RG(object, bc.method = bc.method, offset = offset) : > Object doesn't contain R and G components > > I also notice that the convert routines will convert to NChannelSet but > not from NChannelSet to other types such as used by limma (RGList, MAList). > > I am tempted to now write the data back to file and construct a generic > 2-color data object using limma::read.maimages(). But this seems an odd > thing to do. > > I've also tried getting the data directly to file and then using the > RMAGEML package but it seems to not install due to need for SJava > installed which won't install on either Mac (my workstation) or Linux > Ubuntu 7.10 due to compilation errors in the SJava C code (subject of > another post if needed). > > > How do I use NChannelSet data or convert to RGList or MAList? > > Thanks for any help... >