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

[Leon Yee]

Hi Prashantha,

Prashantha Hebbar Kiradi [MU-MLSC] 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

  As for my understanding, RG$printer implies that you don't have the 
"PrintTip", so you should try plotLoess or likewise.

This error msg indicates the function requires the input be 
243504(912*267) lines, but you provided only 205700.

HTH
Leon