Dear List, I have two questions regarding oligo::crlmm for normalizing/genotyping Affy SNP 6.0 arrays. 1) I want to extract normalized values and I'm using the readSummaries() function after calling crlmm(). I found that the results are quite different from oligo::snprma. I've pasted the first bit of results from my calls to crlmm and snprma below (for extracting normalized A allele info). Maybe I'm using the wrong function from crlmm? But I also can't tell if the normalization function inside crlmm uses the normalizeToHapmap = TRUE setting (I also tested the false setting as well). 2) Ideally, what I would like is to extract normalized SNP and CN probe info. As you can see below, I'm only extracting the 906,600 SNP probes. Is there a way to use oligo functions to retrieve CN probe normalized info? Unfortunately, I cannot upgrade my R version or oligo packages because we're in the final stages of our analysis (which uses genotype info from oligo::crlmm). Thank you kindly, Denise I have checked to make sure that the sample order is the same. > crlmm(files, outputDir, verbose = TRUE); > alleleA <- readSummaries("alleleA", outputDir); > alleleA <- alleleA[order(rownames(alleleA)),]; > str(alleleA) num [1:906600, 1:76] 11.19 10.03 9.99 11.57 10.06 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:906600] "SNP_A-1780270" "SNP_A-1780271" "SNP_A-1780272" "SNP_A-1780274" ... > snprma.results <- snprma(files); > str(A(snprma.results)) num [1:906600, 1:76] 6.29 5.98 6.62 6.19 6.13 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:906600] "SNP_A-1780270" "SNP_A-1780271" "SNP_A-1780272" "SNP_A-1780274" ... sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.genomewidesnp.6_1.1.0 RSQLite_0.9-4 [3] DBI_0.2-5 genomewidesnp6Crlmm_1.0.2 [5] oligo_1.14.0 oligoClasses_1.12.1 [7] Biobase_2.12.1 getopt_1.17 loaded via a namespace (and not attached): [1] AnnotationDbi_1.12.0 Biostrings_2.20.1 IRanges_1.10.4 [4] affxparser_1.24.0 affyio_1.20.0 annotate_1.28.0 [7] bit_1.1-6 crlmm_1.8.7 ellipse_0.3-5 [10] ff_2.2-1 genefilter_1.30.0 mvtnorm_0.9-96 [13] preprocessCore_1.12.0 splines_2.12.1 survival_2.36-2 [16] tools_2.12.1 xtable_1.5-6 [[alternative HTML version deleted]]