[BioC] ImaGene data into limma

Heidi Dvinge s973315 at student.dtu.dk
Thu Apr 8 17:48:46 CEST 2004


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?


[1] 6

[1] 4

[1] 20

[1] 20

  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 ...

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