[BioC] ImaGene data into limma

Gordon K Smyth smyth at wehi.EDU.AU
Thu Apr 8 23:45:35 CEST 2004


> 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 ...



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