[BioC] Error message in imageplot of limma packages

[Matthew Ritchie]

Hi Joyce,

As the error message suggests, the number of spots in your RB/MA object
and the layout you have specified don't agree.  Try

dim(RB$Rb)
dim(MA$M)

to determine how many spots (rows) and arrays (columns) you have read in
and converted to log-ratios.  Does the number of spots returned agree with
the number you have specified in the layout arguments of imageplot()
(12*4*21*21 = 21168)?  If not then you need to correct this so that the
two agree.  Best wishes,

Matt Ritchie

> Hi,
> I tried to use imageplot to see my normalized data in limma package, I
> tried  both command as following,
>> imageplot(log2(RB$Rb[,1]),RB$printer,low="white",high="red")
> and
>> imageplot(MA$M[,1],RB$printer,zlim=c(-3,3))
> and
>>imageplot(MA$M[,1],layout=list(ngrid.r=12,ngrid.c=4,nspot.r=21,nspot.c=21))
>
> they all gave me the same kind of error messages:
> Error in imageplot(log2(RB$Rb[, 1]), RB$printer, low = "white", high =
> "red")  :
>         Number of image spots does not agree with layout dimensions
>
> Or
> Error in imageplot(MA$M[, 1], RB$printer) :
>         Number of image spots does not agree with layout dimensions
>
> Any idea is greatly appreciated!
> Thanks
>
> ********************************
> Joyce Gu   M.S.
> Scientific Programmer
>
> Cancer Genomics Group
> Baylor College of Medicine
> Phone: 832-824-4680
> Fax: 832-825-4038