[BioC] lumi and 450k control probe files

[Oliver Hofmann]

Dear all,


started playing with lumi and samples from Illumina 450k arrays; slowly learning how to process the data. One task I still need to figure out is how to get lumi to accept the control probe information exported from BeadStudio.

Does someone have pointers to the expected data format, or a working script and toy data they wouldn't mind sharing so I can check for differences between my exported files and those that work?

Minimal examples are a bit difficult due to the required files, but maybe I can summarize:

1. Importing exported sample methylation data with lumiMethyR works fine

2. Trying to use the 'controlData' argument fails for the provided control probe file as the import expects a [SAMPLE METHYLATION PROFILE] block which isn't present in the control data:

> lumiData <- lumiMethyR(sampleMeth, lib=annot, controlData=sampleControl)

Error in .getFinalReportBlock(filename, blockname = blockname, blocks = blocks,  : 
  The block called "[SAMPLE METHYLATION PROFILE]" in the file "/data/A_Control_Probe_Profile.txt" is not present and needs to be.  Please re-export from bead studio.

A quick check confirms that the Sample methylation profile block is only present in the sample file, not the control file (as expected):

--
> head -n 10 A_Control_Probe_Profile.tx
[Header]
GSGX Version    1.1.0
Report Date     11/18/2011 5:08:30 PM
Project A
Group Set       A
Analysis        A_nonorm_nobkgd
Normalization   none
[Control Probe Profile]
TargetID        ProbeID 1.Signal_Grn    1.Signal_Red ...
--

3. By concatenating the sample and control probe files I can feed them to methyLumiR, and the methyData at QC gets set correctly; manually converting the resulting object to a MethyLumiM object seems to be causing trouble downstream through. Trying to directly import the merged data file into lumiMethyR fails again

Pointers very much welcome!

Best,

	Oliver

> sessionInfo()

R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C              
[10] 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] RColorBrewer_1.0-5                    IlluminaHumanMethylation450k.db_1.4.6
 [3] org.Hs.eg.db_2.6.4                    RSQLite_0.11.0                       
 [5] DBI_0.2-5                             AnnotationDbi_1.16.10                
 [7] lumi_2.6.0                            nleqslv_1.9.0                        
 [9] methylumi_2.0.1                       Biobase_2.14.0                       

loaded via a namespace (and not attached):
 [1] affy_1.32.0           affyio_1.22.0         annotate_1.32.0       BiocInstaller_1.2.1  
 [5] grid_2.14.0           hdrcde_2.15           IRanges_1.12.5        KernSmooth_2.23-6    
 [9] lattice_0.20-0        MASS_7.3-16           Matrix_1.0-1          mgcv_1.7-9           
[13] nlme_3.1-102          preprocessCore_1.16.0 tools_2.14.0          xtable_1.6-0         
[17] zlibbioc_1.0.0      

--
Skype: ohofmann 	Phone: +1 (617) 365 0984
Associate Director Bioinformatics Core
Harvard School of Public Health
http://compbio.sph.harvard.edu/chb/