Hi Atul

I just had a quick try of the example data you sent. It works pretty well.
Here is my command:

test <- lumiR('FinalReport_sample.txt', annotationColumn =
c('PROBE_ID','ACCESSION','SYMBOL','ENTREZ_GENE_ID','PROBE_START','CHROMOSOME'))

If you still have problems, change the error options and send me the all
error messages:
options(error=recover)


Pan



On Tue, Apr 23, 2013 at 10:49 AM, Atul Kakrana <atulkakrana@outlook.com>wrote:

>  Hi Pan,
>
> Thanks for replying. Please see attached file with first 100 lines of
> FinalReport.txt.
>
> Awaiting response.
>
> AK
>
>
> On 04/23/2013 11:53 AM, Pan Du wrote:
>
>  Hi Atul
>
>  Can you send me to the top 100 rows of your data file? I cannot tell the
> reason without seeing your data. Thanks for reporting this!
>
>  Pan
>
>
>  Date: Mon, 22 Apr 2013 13:28:21 -0400
> From: Atul Kakrana <atulkakrana@outlook.com>
> To: "bioconductor@r-project.org" <bioconductor@r-project.org>
> Subject: [BioC] Lumi problem - 'Annotation columns not available'
> Message-ID: <BLU0-SMTP39586425625757CB11593A1ADCB0@phx.gbl>
> Content-Type: text/plain; charset="ISO-8859-1"
>
> Hello All,
>
> I am trying to input the Illumina Microarray data using 'lumi' but
> getting an error:
>
> > mydata_test <-
> lumiR.batch(filename,sep='\t',convertNuID=FALSE,inputAnnotation=TRUE,
> annotationColumn
> =
> c('PROBE_ID','ACCESSION','SYMBOL','ENTREZ_GENE_ID','
> PROBE_START','CHROMOSOME'))
> Inputting the data ...
> Inputting the data ...
> Annotation columns are not available in the data.
> Perform Quality Control assessment of the LumiBatch object ...
>
> This error is not new to me as I had this problem before as well. But
> that time I ignored it and later in analysis used 'lumiMouseAll.db'
> package for annotations. The final results had incomplete (missing)
> annotations.
>
> This time I really need complete annotations and therefore trying to
> import annotations as provided by Beadstudio rather than using
> 'lumiMouseAll.db'. Please tell me what is the problem as I checked all
> the mentioned columns does exist in rawfile.
>
> >sessionInfo()
>
> R version 2.15.3 (2013-03-01)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> LC_PAPER=C
>  [8] LC_NAME=C                  LC_ADDRESS=C
> LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] lumiMouseIDMapping_1.10.0 illuminaMousev1.db_1.16.1
> illuminaMousev2.db_1.16.1 lumiMouseAll.db_1.18.0
> org.Mm.eg.db_2.8.0        calibrate_1.7.1
> scatterplot3d_0.3-33
>  [8] affyQCReport_1.36.0       lattice_0.20-13
> farms_1.10.0              MASS_7.3-23
> genefilter_1.40.0         R2HTML_2.2
> annotate_1.36.0
> [15] affycoretools_1.30.0      KEGG.db_2.8.0
> affy_1.36.1               GO.db_2.8.0
> RSQLite_0.11.2            DBI_0.2-5
> AnnotationDbi_1.20.7
> [22] limma_3.14.4              lumi_2.10.0
> nleqslv_2.0               Biobase_2.18.0
> BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.26.0         affyPLM_1.34.0        annaffy_1.30.0
> AnnotationForge_1.0.3 BiocInstaller_1.8.3   biomaRt_2.14.0
> Biostrings_2.26.3     Category_2.24.0
>  [9] colorspace_1.2-1      gcrma_2.30.0          gdata_2.12.0
> GOstats_2.24.0        gplots_2.11.0         graph_1.36.2
> grid_2.15.3           GSEABase_1.20.2
> [17] gtools_2.7.0          IRanges_1.16.6        KernSmooth_2.23-10
> Matrix_1.0-11         methylumi_2.4.0       mgcv_1.7-22
> nlme_3.1-108          parallel_2.15.3
> [25] preprocessCore_1.20.0 RBGL_1.34.0           RColorBrewer_1.0-5
> RCurl_1.95-4.1        simpleaffy_2.34.0     splines_2.15.3
> stats4_2.15.3         survival_2.37-4
> [33] tools_2.15.3          XML_3.95-0.2          xtable_1.7-1
> zlibbioc_1.4.0
>
> AK
>
>
>

	[[alternative HTML version deleted]]

