[BioC] limma and marray data import problem

[Gordon K Smyth]

On Wed, 4 Jun 2008, Piotr Stêpniak wrote:

> Dear Gordon,
>
> Thank you very much for your answer. When I try the arguments nrows=2
> or 2640 I get the error:
> Read 15sz_szk10_Results1.gpr

This shows that the first gpr file has read correctly.  Try putting 
file=targets$FileName[1] to read one file at a time.

This shows that your gpr files have a problem after the last line of data.

> Error in read.table(file = file, header = TRUE, col.names = allcnames,  :
>  formal argument "nrows" matched by multiple actual arguments
>
> Csv files give the same error with nrows attribute but the do read
> fine with the following instruction:
> bialkoRaw<- read.maimages( targets$FileName, columns=list(G="Ch1\
> Median", Gb="Ch1\ B\ Median", R="Ch2\ Median", Rb="Ch2\ B\ Median"),
> sep=",")
> And the object is almost fine:

> The columns are not shifted to right, so I get the correct Median
> values as desired.
>
> However there is something wrong with the object because any following
> instructions give this error:
> Error in if (is.int(totalPlate)) { : argument is of length zero
> Preasumably it is because the printer layout is missing,

There's nothing wrong with the object, the printer layout is simply not 
set.  Since limma doesn't "know" the ScanArray csv format, you have to set 
the printer layout yourself manually.

> Is there a way to check RGList object integrity?

Just look at the object, show(RG).

Best wishes
Gordon

> Kind Regards,
> Piotrek