Hi,

I am trying to install GenomeWideSNP_6 using makecdfenv() but I am unable to do so. I keep getting the error 

make.cdf.package("GenomeWideSNP_6.cdf", cdf.path="/USER/Downloads/E-GError in make.cdf.env(filename, cdf.path = cdf.path, compress = compress,  : gpath  makecdfenv does not currently know how to handle cdf files of this type (genotyping).

I am new to BiocLite and SNP analysis in Microarray data. Please help me.

And I did try installing the pd.genomewidesnp.6 using biocLite(pd.genomewidesnp.6) and loading it using library(pd.genomewidesnp.6) but each time I ran eset.mas5 = mas5 (affy.data), I got the following error.

Loading required package: DBI
> affy.data = ReadAffy()
> eset.mas5 = mas5(affy.data)
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...Error in getCdfInfo(object) :
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain GenomeWideSNP_6
Library - package genomewidesnp6cdf not installed
Bioconductor - genomewidesnp6cdf not available

Session Info

sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] pdInfoBuilder_1.38.0 affxparser_1.46.0    RSQLite_2.0
 [4] oligo_1.38.0         Biostrings_2.42.1    XVector_0.14.1
 [7] IRanges_2.8.2        S4Vectors_0.12.2     oligoClasses_1.36.0
[10] affy_1.52.0          Biobase_2.34.0       BiocGenerics_0.20.0
[13] makecdfenv_1.50.0    affyio_1.44.0        BiocInstaller_1.24.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11               GenomeInfoDb_1.10.3
 [3] bitops_1.0-6               iterators_1.0.8
 [5] tools_3.3.3                zlibbioc_1.20.0
 [7] digest_0.6.12              bit_1.1-12
 [9] memoise_1.1.0              preprocessCore_1.36.0
[11] tibble_1.3.3               lattice_0.20-35
[13] ff_2.2-13                  rlang_0.1.1
[15] Matrix_1.2-10              foreach_1.4.3
[17] DBI_0.7                    bit64_0.9-7
[19] grid_3.3.3                 blob_1.1.0
[21] codetools_0.2-15           GenomicRanges_1.26.4
[23] splines_3.3.3              SummarizedExperiment_1.4.0
[25] RCurl_1.95-4.8

Traceback

traceback()
3: .Call("ReadCDFFile", file.path(path.expand(cdf.path), filename),
       PACKAGE = "affyio")
2: make.cdf.env(filename, cdf.path = cdf.path, compress = compress,
       return.env.only = FALSE)
1: make.cdf.package("GenomeWideSNP_6.cdf", cdf.path = "/USER/Downloads/E-GEOD-71522.raw.1",
       compress = FALSE, species = "Homo_sapiens", package.path = pkgpath)

Please help me with this issue.

Thanks.

The MAS5.0 algorithm is intended for expression arrays, but you have a SNP array. If you want to generate SNP calls, you should be using crlmm (in the crlmm package).