[BioC] how to set up sampleInfo for methylation array in illumina 450K

[guest [guest]]

Dear Users,

I tried to use lumi to import the methylation array data from illumina 450k array into R using lumi package, but I could not find the instruction on how to format the sampleInfo file. I just set it as below:

SENTRIX_ID	SENTRIX_BARCODE	SENTRIX_POSITION	Group	ART initiation	Infection
01A00421_NR056388	8691803116	R01C01	HIV-CTR	N	None
01A00068_NR056389	8691803116	R02C01	HIV-CTR	N	None
01A00483_NR056390	8691803116	R03C01	HIV-CTR	N	None
01A00347_NR056391	8691803116	R04C01	HIV-CTR	N	None
01A00060_NR056393	8691803116	R05C01	Medium	N	Pre
01A00065_NR056395	8691803116	R06C01	Medium	N	Post
01A00113_NR056404	8691803116	R01C02	Medium	N	Post
01A00079_NR056406	8691803116	R02C02	Medium	N	Post

After reading the sampleinfo file using read.csv() as below
sampleInfo=read.csv("sampleInfo_12.csv",sep="\t",header=T,stringsAsFactors=F)

I used the function as instructed in the turtorial
My_data=importMethyIDAT(sampleInfo, dataPath = getwd(), lib = NULL, bigMatrix=FALSE, dir.bigMatrix='.')

There is an error message:
Error in importMethyIDAT(sampleInfo, dataPath = getwd(), lib = NULL, bigMatrix = FALSE,  : 
  'SENTRIX_POSITION' and 'SENTRIX_BARCODE' or 'SENTRIX_ID' and are required in 'sampleInfo'!

I don't get it that I already added those required items in the sampleInfo, why does it have this error?

Thanks a lot for the help and I really appreciate it.

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] lumi_2.14.2              BiocInstaller_1.12.1     VariantAnnotation_1.8.13 Rsamtools_1.14.3         Biostrings_2.30.1        GenomicRanges_1.14.4    
 [7] XVector_0.2.0            IRanges_1.20.7           ggplot2_0.9.3.1          phyloseq_1.6.1           picante_1.6-2            nlme_3.1-117            
[13] ape_3.1-1                ade4_1.6-2               knitr_1.5                vegan_2.0-10             lattice_0.20-29          permute_0.8-3           
[19] biom_0.3.12              metagenomeSeq_1.5.47     devtools_1.5             gplots_2.13.0            RColorBrewer_1.0-5       matrixStats_0.8.14      
[25] limma_3.18.13            Biobase_2.22.0           BiocGenerics_0.8.0      

loaded via a namespace (and not attached):
 [1] affy_1.40.0            affyio_1.30.0          annotate_1.40.1        AnnotationDbi_1.24.0   base64_1.1             beanplot_1.1          
 [7] biomaRt_2.18.0         bitops_1.0-6           BSgenome_1.30.0        bumphunter_1.2.0       caTools_1.17           cluster_1.15.2        
[13] codetools_0.2-8        colorspace_1.2-4       DBI_0.2-7              dichromat_2.0-0        digest_0.6.4           doRNG_1.6             
[19] evaluate_0.5.3         foreach_1.4.2          formatR_0.10           gdata_2.13.3           genefilter_1.44.0      GenomicFeatures_1.14.5
[25] grid_3.0.2             gtable_0.1.2           gtools_3.4.0           httr_0.3               igraph_0.7.1           illuminaio_0.4.0      
[31] iterators_1.0.7        itertools_0.1-3        KernSmooth_2.23-12     labeling_0.2           locfit_1.5-9.1         MASS_7.3-31           
[37] Matrix_1.1-3           mclust_4.3             memoise_0.2.1          methylumi_2.8.0        mgcv_1.7-29            minfi_1.8.9           
[43] multtest_2.18.0        munsell_0.4.2          nleqslv_2.1.1          nor1mix_1.1-4          pkgmaker_0.20          plyr_1.8.1            
[49] preprocessCore_1.24.0  proto_0.3-10           R.methodsS3_1.6.1      Rcpp_0.11.1            RCurl_1.95-4.1         registry_0.2          
[55] reshape_0.8.5          reshape2_1.4           RJSONIO_1.2-0.1        rngtools_1.2.4         RSQLite_0.11.4         rtracklayer_1.22.7    
[61] scales_0.2.4           siggenes_1.36.0        splines_3.0.2          stats4_3.0.2           stringr_0.6.2          survival_2.37-7       
[67] tools_3.0.2            whisker_0.3-2          XML_3.95-0.2           xtable_1.7-3           zlibbioc_1.8.0        


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