[BioC] limma and marray data import problem

[Piotr Stępniak]

Dear Gordon,

Thank you again for your prompt reply.

On Wed, Jun 4, 2008 at 10:25 AM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
>
>
> 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.
>

If I do that, how do I put them together later on to have all the
files in one object for further analysis?

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

Is it possible it is because the files have different eof sign? Would
changing them to unix like or windows like be of any help and would it
be considered as data manipulation?

>> 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$FileName, columns=list(G="Ch1\
>> Median", Gb="Ch1\ B\ Median", R="Ch2\ Median", Rb="Ch2\ B\ Median"),
>> sep=",")
>> And the object is almost fine:
>
>> The columns are not shifted to right, so I get the correct Median
>> values as desired.
>>
>> However there is something wrong with the object because any following
>> instructions give this error:
>> Error in if (is.int(totalPlate)) { : argument is of length zero
>> Preasumably it is because the printer layout is missing,
>
> There's nothing wrong with the object, the printer layout is simply not set.
>  Since limma doesn't "know" the ScanArray csv format, you have to set the
> printer layout yourself manually.
>
OK, I do this:
bialkoRaw$printer$ngrid.r=10
bialkoRaw$printer$ngrid.c=4
bialkoRaw$printer$nspot.c=9
bialkoRaw$printer$nspot.r=9
bialkoRaw$printer$spacing=1
bialkoRaw$printer$ndups=3

Is there anything else I should add? When I try to use e.g.
maQualityPlots() I get:
> maQualityPlots(bialkoRaw)
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?

Kind Regards,
Piotr

>> Is there a way to check RGList object integrity?
>
> Just look at the object, show(RG).
>
> Best wishes
> Gordon
>
>> Kind Regards,
>> Piotrek