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/packages/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/


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