Dear Juan, I have never seen this warning message, but my current version of R is still R-2.15.0. Maybe, the R-developers have decided to issue a warning message in R-2.15.1, since I am using the C++ code "cout" for my messages. I am forwarding this to BioC so maybe someone can comment on this issue. Especially, why it says: "partial output only". However, you can definitely ignore this warning message, but is the output indeed only partial? Best regards, Christian On 10/2/12 10:47 PM, Juan Fernandez Tajes wrote: > Dear Christian, > > I?m trying to use xps for analyzing HuGene 1.1 st array from Affymetrix, > I?ve used the following code for creating the root scheme: > > libdir<- "/Users/juane/Investigaci?n/INIBIC/Affymetrix Raw Data/Analisis > xps/libraryfiles" > anndir<- "/Volumes/GigaDrive/Affy/Annotation" > scmdir<- "/Users/juane/Investigaci?n/INIBIC/Affymetrix Raw Data/Analisis > xps/schemes" > > scheme.hugene11stv1.na32 <- import.exon.scheme("hugene11stv1", filedir = > file.path(scmdir, "na32"), > file.path(libdir, > "HuGene-1_1-st-v1_strip_libraryfile", "HuGene-1_1-st-v1.r4.clf"), > file.path(libdir, > "HuGene-1_1-st-v1_strip_libraryfile", "HuGene-1_1-st-v1.r4.pgf"), > file.path(anndir, "Version08Oct", > "HuGene-1_1-st-v1.na32.hg19.probeset.csv"), > file.path(anndir, "Version08Oct", > "HuGene-1_1-st-v1.na32.hg19.transcript.csv")) > > However when I execute the following code for importing the data, I got > a warning: > > data.test <- import.data(scheme.hugene11st, "tmpdt_data.test", > celdir=celdir, celfiles=celfiles, verbose=T) > Importing </users> Data/CEL/10SE208.CEL> as <x10se208.cel>... > hybridization statistics: > 1 cells with minimal intensity 11.5 > 1 cells with maximal intensity 22789.9 > Importing </users> Data/CEL/10SE209.CEL> as <x10se209.cel>... > hybridization statistics: > 5 cells with minimal intensity 12.3 > 1 cells with maximal intensity 22839.2 > Importing </users> Data/CEL/10SE210.CEL> as <x10se210.cel>... > hybridization statistics: > 1 cells with minimal intensity 11.5 > 1 cells with maximal intensity 20892.7 > Importing </users> Data/CEL/10SE211.CEL> as <x10se211.cel>... > hybridization statistics: > 1 cells with minimal intensity 10.5 > 1 cells with maximal intensity 22303.1 > Importing </users> Data/CEL/10SE212.CEL> as <x10se212.cel>... > hybridization statistics: > 2 cells with minimal intensity 11.5 > 1 cells with maximal intensity 20283.4 > Importing </users> Data/CEL/10SE213.CEL> as <x10se213.cel>... > hybridization statistics: > 1 cells with minimal intensity 8.3 > 1 cells with maximal intensity 21714.6 > Importing </users> Data/CEL/10SE214.CEL> as <x10se214.cel>... > hybridization statistics: > 2 cells with minimal intensity 12 > 1 cells with maximal intensity 21296.2 > Importing </users> Data/CEL/10SE215.CEL> as <x10se215.cel>... > hybridization statistics: > 2 cells with minimal intensity 11.8 > 1 cells with maximal intensity 19225.4 > Importing </users> Data/CEL/10SE216.CEL> as <x10se216.cel>... > hybridization statistics: > 2 cells with minimal intensity 11.5 > 1 cells with maximal intensity 21394.9 > Importing </users> Data/CEL/10SE218.CEL> as <x10se218.cel>... > hybridization statistics: > 1 cells with mini > (WARNING: partial output only, ask package author to use Rprintf instead!) > mal intensity 12.8 > 1 cells with maximal intensity 21774.8 > > I think when I build the root.scheme for HuGene 1.1 st I got a similar > warning, > > Is this warning an important issue? > > Many thanks > > Juan > >