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

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