Hi

I guess you didn't input the sampleInfo correctly. Based on your
filename "sampleInfo_12.csv",
it is a csv file, not a Tab delimited file. So try to import the file using
read.csv function.

I also noticed there are "SENTRIX_ID" columns together with "SENTRIX_BARCODE"
and "SENTRIX_POSITION". The importMethyIDAT function assumes the "SENTRIX_ID"
is a combination of "SENTRIX_BARCODE" and "SENTRIX_POSITION". But looks
like your data does not meet this assumption. So please remove the "SENTRIX_ID"
column.

Tell me if the problem still exists.

Pan


On Tue, Apr 29, 2014 at 10:29 AM, guest [guest] <guest@bioconductor.org>wrote:

>
> 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
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>

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