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Edo Plantinga
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50
@edo-plantinga-524
Last seen 10.2 years ago
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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