[BioC] Lumi problem - 'Annotation columns not available'

[Atul Kakrana]

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