[BioC] RMA probe summarization when sizes of probesets are unequal
Xin Lin [guest]
guest at bioconductor.org
Fri Aug 16 17:50:04 CEST 2013
Dear all,
I have a customized two-channel microarray designed by NimbleGen (one of the last they produced) based on 26981 cDNA sequences of tomato. 60-mer oligonucleotide probes were designed and multiple probes were used for each transcript. The problem is, the sizes of probe-sets are not equal -- ranging from 5 to 1 (26784 of them have 5 probes).
I am now trying to use rma() in oligo for normalization and summarization. My question is, in the situation where sizes of probe-sets are unequal, how does rma() do the probe summarization? Will it be problematic if I use rma() directly? If rma() could not do the correct job, what alternative method can I use for probe summarization?
I am new in microarray and R, and I'll appreciate your help very much! Thank you for your time!
Xin
-- 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] qvalue_1.34.0 affyPLM_1.36.0 preprocessCore_1.22.0
[4] gcrma_2.32.0 affy_1.38.1 pd.121114.slycop.tm.exp_0.0.1
[7] pdInfoBuilder_1.24.0 affxparser_1.32.3 oligo_1.24.0
[10] oligoClasses_1.22.0 geneplotter_1.38.0 lattice_0.20-15
[13] annotate_1.38.0 AnnotationDbi_1.22.6 Biobase_2.20.1
[16] BiocGenerics_0.6.0 RColorBrewer_1.0-5 limma_3.16.6
[19] genefilter_1.42.0 RSQLite_0.11.4 DBI_0.2-7
loaded via a namespace (and not attached):
[1] affyio_1.28.0 BiocInstaller_1.10.2 Biostrings_2.28.0 bit_1.1-10
[5] codetools_0.2-8 ff_2.2-11 foreach_1.4.1 GenomicRanges_1.12.4
[9] grid_3.0.1 IRanges_1.18.2 iterators_1.0.6 splines_3.0.1
[13] stats4_3.0.1 survival_2.37-4 tcltk_3.0.1 tools_3.0.1
[17] XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.6.0
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