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.
Thanking you in anticipation,
Prashantha
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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
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
