Hi list, I am using the marray package to read in two-color cDNA array data (R 1.9.1, marray 1.5.14, linux). When I try: >theLayout = new("marrayLayout", maNgr=8, maNgc=4, maNsr=24, maNsc=24) >a= read.marrayRaw(files, name.Gf="CH1I", name.Gb= "CH1B", name.Rf="CH2I", name.Rb="CH2B", layout=theLayout) a is a marrayRaw object with only one spot. When I omit the layout in the read.marrayRaw call and assign it later, it seems to work fine: >a= read.marrayRaw(files, name.Gf="CH1I", name.Gb= "CH1B", name.Rf="CH2I", name.Rb="CH2B") > a@maLayout <- theLayout In my older R version (R 1.9.0, marray 1.5.8) the first call also worked. Now my question is: Has the read.marrayRaw function changed in some way (I haven`t found anything in the documentation), is it a bug or something else still? Any help or information is highly appreciated, Julia

Hi Julia, This is a recently discovered bug, one of the function calculate the number of rows wronly when the layout parameter is there. The current fix is to do exactly what you have propose. I will fix it ASAP. Cheers Jean > I am using the marray package to read in two-color cDNA array data (R > 1.9.1, marray 1.5.14, linux). > When I try: > >theLayout = new("marrayLayout", maNgr=8, maNgc=4, maNsr=24, maNsc=24) > >a= read.marrayRaw(files, name.Gf="CH1I", name.Gb= "CH1B", > name.Rf="CH2I", name.Rb="CH2B", layout=theLayout) > a is a marrayRaw object with only one spot. > > When I omit the layout in the read.marrayRaw call and assign it later, > it seems to work fine: > >a= read.marrayRaw(files, name.Gf="CH1I", name.Gb= "CH1B", > name.Rf="CH2I", name.Rb="CH2B") > > a@maLayout <- theLayout > > In my older R version (R 1.9.0, marray 1.5.8) the first call also worked. > Now my question is: Has the read.marrayRaw function changed in some way > (I haven`t found anything in the documentation), is it a bug or > something else still? > > Any help or information is highly appreciated, > Julia > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >