[BioC] using beadarray or limma without spatial information

[Wei Shi]

Dear Sashank,

No, read.ilmn from limma can only read in summary level data (probe data). The limma analysis on Illumina WG BeadChips always starts from probe level data. The limma users guide provides a case study for the analysis of BeadChip data.

Hope this helps.


Best wishes,

Wei


On Jun 4, 2013, at 6:16 AM, Sashank K.[guest] wrote:

> 
> Hello, I am rather new to microarray processing in general, and I have recently worked through the BeadArrayUseCases vignette.  I have bead level data with the format below (two columns containing the Probe IDs and intensity levels).  Below is an example of the format:
> 
> Code	Grn
> 10008	850
> 10008	1023
> 10008	1035
> ...     ...
> 
> The BeadChip is of the Human WG6-v3 variety, and I have several of these that I want to include in my analysis.  As you can see, I do not have the spatial information, and will likely not be able to do many of the quality analyses contained in the vignette on my own data, but I'd still like to construct summary level data, calculating the average, correcting for batch effects, normalizing, etc.  When I try to read my data into R using readIllumina after formatting the sampleSheet correctly, I get the following error:
> 
> Error in `[.data.frame`(lines, 1, 1:4) : undefined columns selected.
> 
> I think it's looking for 4 columns in my files; basically it wants the file to contain the x and y coordinates of the beads.  Is there anyway to get readIllumina to read my data, or is there another package or function that I should use?  Again, the main thing I want to do is get an average of for each the bead replicates, normalize the data, correct for batch effects, etc. given data of the format I have.
> 
> Should I be using a different package?  I don't think read.ilmn from limma can read raw bead-level data of the format above.  Again, please bear in mind that I am brand new at any of this and in fact come from the structural world.
> 
> -- output of sessionInfo(): 
> 
> R version 3.0.1 RC (2013-05-12 r62742)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
> [1] C
> 
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods  
> [8] base     
> 
> other attached packages:
> [1] beadarray_2.10.0   ggplot2_0.9.3.1    Biobase_2.20.0     BiocGenerics_0.6.0
> 
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.22.5 BeadDataPackR_1.12.0 DBI_0.2-7           
> [4] IRanges_1.18.1       MASS_7.3-26          RColorBrewer_1.0-5  
> [7] RSQLite_0.11.3       colorspace_1.2-2     dichromat_2.0-0     
> [10] digest_0.6.3         grid_3.0.1           gtable_0.1.2        
> [13] labeling_0.1         limma_3.16.3         munsell_0.4         
> [16] plyr_1.8             proto_0.3-10         reshape2_1.2.2      
> [19] scales_0.2.3         stats4_3.0.1         stringr_0.6.2    
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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