[BioC] limma and marray data import problem

[Piotr Stępniak]

Dear Gordon,

Thank you VERY much for all your answers. One more question and I
should be able to proceed with my analysis:

>> Error: dims [product 2641] do not match the length of object [3240]
>> In addition: Warning message:
>> In samplesub & which & subset & good :
>>  longer object length is not a multiple of shorter object length
>>
>> Which is because the array has 36 grids instead of 40 (it is not a
>> full rectangle). Is there a way to go around this situation? Maybe I
>> can set a grid number value?
>
> There is no way to set the print layout in limma.  limma strictly assumes
> complete arrays.  You'd have to pad out your data object with NAs for the
> other 4 grids if you want to use print layout functions in limma.
>
> You do not need the layout to create MA-plots or to loess normalize.
>

Could you please advice on the best way to pad out the object with
NAs? I tried this:
bialkoRaw[2641:3240,]<- read.maimages( targets$FileName[1],
columns=list(G="Ch1\ Median", Gb="Ch1\ B\ Median", R="Ch2\ Median",
Rb="Ch2\ B\ Median"), sep=",", na.strings="NA", blank.lines.skip =
FALSE)

and I did not get any additional columns or rows written.

Kind Regards,
Piotr