Entering edit mode
Abhilash Venu
▴
340
@abhilash-venu-2680
Last seen 10.2 years ago
Hi all,
I was trying background correction for array CGH data using snapCGH.
While
performing the backgroundCorrection using normexp, which has given me
the
the following error. Could you suggest some solution.
>RG1<-read.maimages("test1.txt",source="agilent")
> RG2 <- backgroundCorrect(RG1, method = "normexp")
Green channel
Corrected array 1
Red channel
Error in if (all(abs(delta) < 1e-10)) break :
missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In log(1 - alpha * theta) : NaNs produced
2: In log(1 - alpha * theta) : NaNs produced
sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] splines grid tools stats graphics grDevices utils datasets methods
base
other attached packages:
[1] snapCGH_1.8.0 aCGH_1.14.0 sma_0.5.15 multtest_1.16.1
cluster_1.11.10
[6] GLAD_1.16.0 DNAcopy_1.14.0 tilingArray_1.18.0 pixmap_0.4-9
geneplotter_1.18.0
[11] annotate_1.18.0 xtable_1.5-2 AnnotationDbi_1.2.1 RSQLite_0.6-8
DBI_0.2-4
[16] genefilter_1.20.0 survival_2.34-1 vsn_3.6.0 lattice_0.17-6
strucchange_1.3-3
[21] sandwich_2.1-0 zoo_1.5-4 RColorBrewer_1.0-2 affy_1.18.1
preprocessCore_1.2.0
[26] affyio_1.8.0 Biobase_2.0.1 limma_2.14.3
loaded via a namespace (and not attached):
[1] KernSmooth_2.22-22
Thanks in advance
--
Regards,
Abhilash
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