Hi I have a question concerning reading ImaGene data into limma (which by the way is a very nice package!). In my experiment I?m using arrays which have a 4x6 metagrid printed twice on each slide, with a little spacing between them. (Similar to the print layout (ngrid.r=12, ngrid.c=4, nspot.r=20, nspot.c=20, ndups=2, spacing=9600, npins=24, start="topleft")) When creating the grid using ImaGene the easiest thing is to make one 4x6 metagrid and then just duplicate it (due to the spacing between them). In the output file there is a column called ?Field?, where the two metagrids are then designed for example A and B. ngrid.r and ngrid.c just runs between 6 and 4 then. However when I read in the data using read.imagene, only the data from the first field is read (see example of output below). Can I work my way around this somehow, or do I have to change the files into having a 4x12 metagrid? I suspect that there is a function for this since the print layout is automatically extracted from ImaGene files, but I haven?t been able to find it. Any suggestions? Thanks \Heidi $printer $ngrid.r [1] 6 $ngrid.c [1] 4 $nspot.r [1] 20 $nspot.c [1] 20 $genes Field Meta Row Meta Column Row Column Gene ID 1 A 1 1 1 1 Control 2 A 1 1 1 2 Control 3 A 1 1 1 3 Control 4 A 1 1 1 4 Control 5 A 1 1 1 5 Control 9595 more rows ...

> Hi > > I have a question concerning reading ImaGene data into limma (which by > the way is a very nice package!). > > In my experiment I?m using arrays which have a 4x6 metagrid printed > twice on each slide, with a little spacing between them. (Similar to the > print layout (ngrid.r=12, ngrid.c=4, nspot.r=20, nspot.c=20, ndups=2, > spacing=9600, npins=24, start="topleft")) > > When creating the grid using ImaGene the easiest thing is to make one > 4x6 metagrid and then just duplicate it (due to the spacing between > them). In the output file there is a column called ?Field?, where the > two metagrids are then designed for example A and B. ngrid.r and ngrid.c > just runs between 6 and 4 then. > > However when I read in the data using read.imagene, only the data from > the first field is read (see example of output below). Can I work my way > around this somehow, or do I have to change the files into having a 4x12 > metagrid? I suspect that there is a function for this since the print > layout is automatically extracted from ImaGene files, but I haven?t been > able to find it. Thanks for the information about Imagene fields. Unfortunately limma only supports a single field for Imagene data files. When I wrote the imagene read functions I didn't know that Imagene files could have multiple fields and so didn't allow for it. Have been planning to fix it, but haven't found the time. Gordon > Any suggestions? > Thanks > > \Heidi > > $printer > $ngrid.r > [1] 6 > > $ngrid.c > [1] 4 > > $nspot.r > [1] 20 > > $nspot.c > [1] 20 > > $genes > Field Meta Row Meta Column Row Column Gene ID > 1 A 1 1 1 1 Control > 2 A 1 1 1 2 Control > 3 A 1 1 1 3 Control > 4 A 1 1 1 4 Control > 5 A 1 1 1 5 Control > 9595 more rows ...