[BioC] Limma: normalizeWithinArrays: Subscript out of bounds

[Edo Plantinga]

Dear all,

In our lab we use cy3 and cy5 landmarks to be able to distinguish between subgrids when performing the image analysis. Because these values will influence a Lowess normalization, I filter out these spots before performing the normalization. The problem is that after I do that and try to normalize with the data that is left, I get an an error that the subscript is out of bounds:

> types
                     SpotType                     Gene ID        col cex
1                        Gene                           *     grey10 0.2
2                 Buffer only                 Buffer only      brown 0.2
3                         Cot                        Cot*     yellow 0.2
4                       Alien                      alien*       pink 0.2
5               Cy-3 landmark               Cy-3 landmark      green 0.2
6               Cy-5 landmark               Cy-5 landmark        red 0.2
7                       Empty                       Empty       blue 0.2
8                   poly d(A)                   poly d(A)   darkblue 0.2
9 Randomized negative control Randomized negative control chocolate1 0.2
> MANoLandmarks <- RG[RG$genes [, "Status"] !="Cy-3 landmark",]
> MANoLandmarks <- MANoLandmarks[MANoLandmarks$genes [, "Status"] !="Cy-5 landmark",]
> # Attributes for printing of control spots are not copied.
> # I am not sure why this happens, but this seems to solve the problem:
> MANoLandmarks$genes$Status <- controlStatus(types,MANoLandmarks)
Matching patterns for: Gene ID 
Found 25056 Gene 
Found 223 Buffer only 
Found 96 Cot 
Found 1920 Alien 
Found 0 Cy-3 landmark 
Found 0 Cy-5 landmark 
Found 336 Empty 
Found 0 poly d(A) 
Found 384 Randomized negative control 
Setting attributes: values col cex 
> MANormalized <- normalizeWithinArrays(MANoLandmarks, method="printtiploess")
Error: subscript out of bounds

Any suggestions?

Kind regards,

Edo Plantinga
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