Hi

It has been awhile since I used the lumi package and my old script does not work any more. I have tried to find out why but without luck. I am trying to load a GenomStudio file (SampleProbeProfile_non-normalized_GeneSpring.txt)

using lumiR

(dataSet <- lumiR(dataFil, sep = NULL, detectionTh = 0.5, na.rm = TRUE, convertNuID = FALSE, lib.mapping = illuminaHumanv3.db, dec = '.', parseColumnName=FALSE, checkDupId=TRUE, QC=TRUE, columnNameGrepPattern = list(exprs='AVG_SIGNAL', se.exprs='BEAD_STDEV', detection='Detection', beadNum='Avg_NBEADS'), inputAnnotation=FALSE, annotationColumn=c(),verbose=TRUE) )

And I get the following error message:
Perform Quality Control assessment of the LumiBatch object ...
Warning message:
In lumiR(dataFil, sep = NULL, detectionTh = 0.5, na.rm = TRUE, convertNuID = FALSE,  :
  The data file may not be in the Illumia BeadStudio or GenomeStudio output format.


My sessionInfo:
sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32

locale:
[1] LC_COLLATE=Norwegian (Bokmål)_Norway.1252  LC_CTYPE=Norwegian (Bokmål)_Norway.1252    LC_MONETARY=Norwegian (Bokmål)_Norway.1252
[4] LC_NUMERIC=C                               LC_TIME=Norwegian (Bokmål)_Norway.1252

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

other attached packages:
 [1] illuminaHumanv3BeadID.db_1.6.0 org.Hs.eg.db_2.4.1             GOstats_2.14.0                 graph_1.26.0
 [5] Category_2.14.0                statmod_1.4.6                  lumi_1.14.0                    MASS_7.3-6
 [9] preprocessCore_1.10.0          mgcv_1.6-2                     affy_1.26.1                    annaffy_1.20.0
[13] KEGG.db_2.4.1                  GO.db_2.4.1                    RSQLite_0.9-2                  DBI_0.2-5
[17] annotate_1.26.1                AnnotationDbi_1.10.2           Biobase_2.8.0                  xtable_1.5-6
[21] RColorBrewer_1.0-2             limma_3.4.4

loaded via a namespace (and not attached):
 [1] affyio_1.16.0      genefilter_1.30.0  grid_2.11.1        GSEABase_1.10.0    lattice_0.18-8     Matrix_0.999375-39 nlme_3.1-96
 [8] RBGL_1.24.0        splines_2.11.1     survival_2.35-8    tools_2.11.1       XML_3.1-1
>

My traceback:
> traceback()
No traceback available

Any idea why?

Regards,
Ingrid


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