affy package and SNP arrays
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Entering edit mode
@vincent-j-carey-jr-4
Last seen 8 weeks ago
United States

Howdy. There is now a github repo for the affy package where a question about processing SNP6 chips with rma was raised. I am posting this issue here to indicate to the world that IMHO crlmm is the package to use for preprocessing affy SNP chips -- but I have not kept close watch on this topic and others may have better information. I can confirm that

BiocManager::install("crlmm")
BiocManager::install('genomewidesnp6Crlmm')
BiocManager::install("hapmapsnp6")
library(crlmm)
example(snprma2)

works with

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
[1] hapmapsnp6_1.42.0         genomewidesnp6Crlmm_1.0.7
[3] crlmm_1.58.0              preprocessCore_1.62.1    
[5] oligoClasses_1.62.0       affy_1.78.0              
[7] Biobase_2.60.0            BiocGenerics_0.46.0      

loaded via a namespace (and not attached):
 [1] Matrix_1.5-4.1              bit_4.0.5                  
 [3] limma_3.56.2                compiler_4.3.0             
 [5] BiocManager_1.30.21         crayon_1.5.2               
 [7] Rcpp_1.0.10                 SummarizedExperiment_1.30.2
 [9] ellipse_0.4.5               bspm_0.5.2                 
[11] GenomicRanges_1.52.0        bitops_1.0-7               
[13] Biostrings_2.68.1           parallel_4.3.0             
[15] VGAM_1.1-8                  splines_4.3.0              
[17] IRanges_2.34.0              lattice_0.21-8             
[19] XVector_0.40.0              S4Arrays_1.0.1             
[21] RcppEigen_0.3.3.9.3         GenomeInfoDb_1.36.0        
[23] ff_4.0.9                    iterators_1.0.14           
[25] DelayedArray_0.26.3         MatrixGenerics_1.12.0      
[27] openssl_2.0.6               GenomeInfoDbData_1.2.7     
[29] DBI_1.1.3                   affyio_1.70.0              
[31] illuminaio_0.42.0           base64_2.0.1               
[33] zlibbioc_1.46.0             foreach_1.5.2              
[35] grid_4.3.0                  mvtnorm_1.2-2              
[37] askpass_1.1                 beanplot_1.3.1             
[39] S4Vectors_0.38.1            codetools_0.2-19           
[41] stats4_4.3.0                RCurl_1.98-1.12            
[43] matrixStats_1.0.0           tools_4.3.0
crlmm hapmapsnp6 genomewidesnp6Crlmm affy • 764 views
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Entering edit mode

aroma.affymetrix is available on CRAN and can be used for SNP6; however, I think that it ultimately uses quite a few Bioconductor packages behind the scenes.

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