If you are trying to analyse data from GEO, it might be best to use the
Geoquery package. The data could have been pre-processed before uploading,
so no longer in the standard format that lumi expects.

You will not be able to read idat files in lumi.

Best wishes,

Mark
On Thursday, June 13, 2013, Joanne [guest] <guest@bioconductor.org> wrote:
>
> Hi,
>
> I've been trying to read in Illumina's *.idat file to no success.
>
> Both of my data are from this platform:-
> Illumina HumanHT-12 V3.0 expression beadchip
>
> I suspect that this may be caused by the version of R that I am using and
so has switched from R version 3.0.1 (2013-05-16) -- "Good Sport" to R
version 2.10.1 (2009-12-14) to see if it works but the same error persist.
>
> This is the sample of my dataset from GSE21973_non-normalized.txt:-
> D_REF   HSC rep1        Detection Pval  HSC rep2        Detection Pval
 HSC rep3        Detection Pval  MPP rep1        Detection Pval  MPP rep2
     Detection Pval  MPP rep3        Detection Pval  MLP rep1
 Detection Pval  MLP rep2        Detection Pval  MLP rep3        Detection
Pval  CMP rep1        Detection Pval  CMP rep2        Detection Pval  CMP
rep3        Detection Pval  GMP rep1        Detection Pval  GMP rep2
 Detection Pval  MEP rep1        Detection Pval  MEP rep2        Detection
Pval
> ILMN_1910180    136.4   0.12253 116.6   0.55468 133.3   0.19368 115.9
0.42951 122.2   0.33202 141.8   0.07905 161.4   0.05138 119     0.5336
 129.9   0.3386  128.5   0.11726 123.1   0.31225 131.6   0.31884 142
0.1581  159.4   0.10013 162.2   0.07115 137.8   0.27009
> ILMN_1725881    164.9   0.01713 168.8   0.01186 141.9   0.09486 110.7
0.62187 161.5   0.01713 172.6   0.01054 211.5   0.00659 143.1   0.04743
170.7   0.00527 143.4   0.02767 166.1   0.01845 154     0.06983 198.2
0.00395 200.6   0.01581 169.4   0.0448  146.7   0.13307
> ILMN_1804174    141.1   0.08169 140.4   0.05929 126.8   0.33465 124.7
0.17523 143.3   0.05665 128.4   0.22793 157.1   0.07115 141.7   0.05665 130
    0.3386  120     0.31094 140.8   0.07246 157.5   0.05402 151.2   0.06588
135.4   0.51383 142.4   0.2859  132.1   0.40053
>
> These are the codes and errors from R:-
>
>> require(lumi)
> Loading required package: lumi
> Loading required package: annotate
> Loading required package: AnnotationDbi
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: affy
> Loading required package: mgcv
> This is mgcv 1.6-1. For overview type `help("mgcv-package")'.
> Loading required package: preprocessCore
> Loading required package: RSQLite
> Loading required package: DBI
> Loading required package: MASS
>
>> lumiR("GSM513193_4674281056_L_Grn.idat")
> Error in gregexpr("\t", dataLine1) : invalid 'text' argument
> In addition: Warning message:
> In readLines(fileName, n = 20) :
>   incomplete final line found on 'GSM513193_4674281056_L_Grn.idat'
>> lumiR("GSE21973_non-normalized.txt")
> Error in gregexpr("\t", dataLine1) : invalid 'text' argument
>
> Can you please advise me on which packages to install for it to work?
>
> Thanks.
>
>  -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.10.1 (2009-12-14)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] lumi_1.12.4          MASS_7.3-4           RSQLite_0.9-2
 DBI_0.2-5            preprocessCore_1.8.0 mgcv_1.6-1           affy_1.24.2
>  [8] annotate_1.24.1      AnnotationDbi_1.8.2  Biobase_2.6.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0      grid_2.10.1        lattice_0.17-26
 Matrix_0.999375-33 nlme_3.1-96        tools_2.10.1       xtable_1.5-6
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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