Hi Apologies if this is a stupid question, but I am just trying to figure out the internal workings of the marray* classes. OK, lets say I have a genepix results file, so in that file I have Block, Column, Row, ID, Name and Expression values. Now lets say I also have an annotation file that has spot annotations in it. This also has Block, Column, Row and then gene annotation columns. Now as I understand it, what I should do is: 1) create a layout object using read.marrayLayout 2) read in the annotations file using read.marrayInfo 3) read in the gpr file using read.GenePix setting the layout parameter to the layout object I created and the gnames parameter to the marrayInfo object I created. Now, what I want to know is this - DOES read.GenePix associate spot annotations to expression values using Block, Column and Row, or does it associate them based on the order of rows in the file? Put another way, if my spot annotation file is ordered alphabetically on, say, gene name, and my gpr file is ordered on (Block, Column, Row), will I associate the wrong gene names with the wrong spots? Put a third way, does my annotation file that I read into marrayInfo object have to have the spots in the SAME ORDER as the genepix results file? Thanks Mick

1) create a layout object using read.marrayLayout 2) read in the annotations file using read.marrayInfo 3) read in the gpr file using read.GenePix setting the layout parameter to the layout object I created and the gnames parameter to the marrayInfo object I created. > Now, what I want to know is this - DOES read.GenePix associate spot > annotations to expression values using Block, Column and Row, or does > it associate them based on the order of rows in the file? Put another > way, if my spot annotation file is ordered alphabetically on, say, > gene name, and my gpr file is ordered on (Block, Column, Row), will I > associate the wrong gene names with the wrong spots? Put a third way, > does my annotation file that I read into marrayInfo object have to > have the spots in the SAME ORDER as the genepix results file? Yes. I usually create the layout information using the same gpr files. YOu can read a gpr file in with the function read.Galfile and that will return a list of two components 1) Layout parameter 2) Gene Names annotation. Cheers Jean

Hi, read.GenePix reads in the data from a genepix gpr file row by row. Genepix gpr files have a standard nesting order of: Columns nested within Rows nested within Blocks. If the nesting order from a third party gal file gene list is different and you use read.marrayInput on the gal file associated with multiple gpr files then your annotations Names and ID's will not match your gpr data. Since one gal file will generally be associated with many gpr data files, you just need to make the nesting order the same so the genes match the data, or run read.marrayInput on one of your gpr data since the Names and ID's are also in the gpr datafile in the correct order. marcus >>> "michael watson (IAH-C)" <michael.watson@bbsrc.ac.uk> 28/08/2003 10:36:12 PM >>> Hi Apologies if this is a stupid question, but I am just trying to figure out the internal workings of the marray* classes. OK, lets say I have a genepix results file, so in that file I have Block, Column, Row, ID, Name and Expression values. Now lets say I also have an annotation file that has spot annotations in it. This also has Block, Column, Row and then gene annotation columns. Now as I understand it, what I should do is: 1) create a layout object using read.marrayLayout 2) read in the annotations file using read.marrayInfo 3) read in the gpr file using read.GenePix setting the layout parameter to the layout object I created and the gnames parameter to the marrayInfo object I created. Now, what I want to know is this - DOES read.GenePix associate spot annotations to expression values using Block, Column and Row, or does it associate them based on the order of rows in the file? Put another way, if my spot annotation file is ordered alphabetically on, say, gene name, and my gpr file is ordered on (Block, Column, Row), will I associate the wrong gene names with the wrong spots? Put a third way, does my annotation file that I read into marrayInfo object have to have the spots in the SAME ORDER as the genepix results file? Thanks Mick _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor ______________________________________________________ The contents of this e-mail are privileged and/or confidential to the named recipient and are not to be used by any other person and/or organisation. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail.