[BioC] limma and marray data import problem

[Piotr Stępniak]

Hello Everyone,

If anyone was following this thread we have found what is wrong with
the gpr files produced by our ScanArrayExpress software that makes
them impossible to read by limma or marray:

It turned out each data row has additional tabulation before the new
line sign but after the last value in the row. This somehow makes for
example read.GenePix() fail with error duplicate row.names not allowed
even though row.names is set to NULL.

My question is if automatic batch removal of aforementioned
tabulations is considered a data manipulation? After all we are just
fixing what the software did wrong on the output, no values are
changed.

Kind Regards,
Piotr Stępniak

On Thu, Jun 5, 2008 at 9:45 AM, Piotr Stępniak
<piotrek.stepniak at gmail.com> wrote:
> 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
>