[BioC] lumiR error on *.idat and *.txt formated file

[Joanne [guest]]

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 

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