Hi, I've been using the crlmm package to do GWAS on Affy snp 6.0 arrays and I have 2 problems: 1) I seem to get NAs for the chi squared and p-value of some SNP IDs. I get this with my data (16 arrays) but also with the data available in the hapmapsnp6 package after following the 'crlmm to downstream data analysis' procedure (available at http://www.bioconductor.org/pac kages/2.10/bioc/vignettes/crlmm/inst/doc/gtypeDownstream.pdf). 2) For my data and the hapmapsnp6 data I can only perform the gwas with a base model with one intercept: gwas <- snp.rhs.tests(ex~1, family="gaussian", link="identity", data=subjdata, snp.data=crlmmSM) Every time I try to follow the example provided in the above pdf: gwas <- snp.rhs.tests(ex~male, data=subjdata, snp.data=crlmmSM, family="gaussian") I get and error message: Warning message: In snp.rhs.tests(ex ~ male, data = subjdata, snp.data = crlmmSM, : Variable(s) in the base model were aliased and have been dropped Can anybody help? Thanks in advance! Maria Traka > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] splines stats graphics grDevices datasets utils methods [8] base other attached packages: [1] GGdata_1.0.19 illuminaHumanv1.db_1.12.2 [3] org.Hs.eg.db_2.7.1 RSQLite_0.11.2 [5] DBI_0.2-5 AnnotationDbi_1.18.4 [7] GGBase_3.18.0 snpStats_1.6.0 [9] Matrix_1.0-9 lattice_0.20-10 [11] survival_2.36-14 hapmapsnp6_1.3.7 [13] crlmm_1.14.3 Biobase_2.16.0 [15] BiocGenerics_0.2.0 oligoClasses_1.18.0 [17] RWinEdt_2.0-0 loaded via a namespace (and not attached): [1] affyio_1.24.0 annotate_1.34.1 BiocInstaller_1.4.7 [4] Biostrings_2.24.1 bit_1.1-8 codetools_0.2-8 [7] ellipse_0.3-7 ff_2.2-7 foreach_1.4.0 [10] genefilter_1.38.0 grid_2.15.1 IRanges_1.14.4 [13] iterators_1.0.6 mvtnorm_0.9-9992 preprocessCore_1.18.0 [16] stats4_2.15.1 tools_2.15.1 XML_3.95-0.1 [19] xtable_1.7-0 zlibbioc_1.2.0 Maria Traka, PhD, MSc Food & Health Programme Science Manager, Institute of Food Research, NR4 7UA, UK Tel: +44 (0) 1603 255194 Fax: +44 (0) 1603 507723 e-mail: maria.traka@ifr.ac.uk<mailto:maria.traka@bbsrc.ac.uk> www.ifr.ac.uk www.foodandhealthnetwork.com e-disclaimer at http://www.ifr.ac.uk/edisclaimer/ [[alternative HTML version deleted]]