[BioC] Error in getting MA plot with plotPrintTipLoess command for 244K chip data

[Sean Davis]

On Thu, Dec 18, 2008 at 7:32 AM, Prashantha Hebbar Kiradi [MU-MLSC]
<prashantha.hebbar at manipal.edu> wrote:
> Dear Friends,
>
> I have a critical error in getting MA plot for agilent 244K chip data with plotPrintTipLoess command. Following are the steps which I followed to get the layout information from my GAL file.
>
>> gal <- readGAL("014791_D_20080424.gal")
>> RG$printer<-getLayout(gal)
>> RG$printer
> $ngrid.r
> [1] 1
>
> $ngrid.c
> [1] 1
>
> $nspot.r
> [1] 912
>
> $nspot.c
> [1] 267
>
> attr(,"class")
> [1] "PrintLayout"
>
> When I use following command to get MA plot with PrinTipLoess, It gives blank MA plot along with error information.
>
>> plotPrintTipLoess(MA, array=1, layout=RG$printer)
> Error in data.frame(y = object$M[, array], x = object$A[, array], gr = factor(gridc(layout)),  :
>  arguments imply differing number of rows: 205700, 243504
>
> I request community to help me to come out this error.

Agilent uses an orange-packed array format (not a grid), so the
concept of rows and columns does not fit the actual layout.  Also,
Agilent does not use print tips, so there is no need to use printTip
in anything manufactured by Agilent (at least not in the past 4 years
or so).

Sean