[BioC] microarray outlier detection

[guest [guest]]

Dear users,

I have human gene 2.0 st array, total 12 samples including 4 groups, each group has 3 replicates. The lab person would like to remove one from each of the group due to the outliers, but from PCA plot, the samples are not clustered, it is hard to remove any sample as an outlier. I wonder if we have the package or function to solve the outlier detection issue on microarray.

Thanks,


 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pd.hugene.2.0.st_3.8.0                oligo_1.24.1                          oligoClasses_1.22.0                   hugene20sttranscriptcluster.db_2.12.1
 [5] org.Hs.eg.db_2.9.0                    RSQLite_0.11.4                        DBI_0.2-7                             AnnotationDbi_1.22.6                 
 [9] Biobase_2.20.1                        BiocGenerics_0.6.0                    limma_3.16.6                         

loaded via a namespace (and not attached):
 [1] affxparser_1.32.3     affyio_1.28.0         BiocInstaller_1.10.3  Biostrings_2.28.0     bit_1.1-10            codetools_0.2-8      
 [7] ff_2.2-11             foreach_1.4.1         GenomicRanges_1.12.4  IRanges_1.18.2        iterators_1.0.6       preprocessCore_1.22.0
[13] splines_3.0.1         stats4_3.0.1          zlibbioc_1.6.0       

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