[BioC] Analysis of chIP-chip

[John H [guest]]

Hi,

A quick question re: data visualisation.

I have three tiling arrays, with input and chIP channels. I've run through the commands as outlined in the vignette, substituting bits and pieces to suit my own data, however, I'm having one problem. When I visualise a plot of the smoothed (i.e. preprocessed data, any method), I get a plot output with two data sets - 1)input and 2) chip.

I was under the assumption that I should only be seeing the chIP dataset, with the input having been taken into account during preprocessing and not displayed on the graph. Assuming that this 'input' data is mainly background (as it is the sample prior to antibody-aided pulldown), how do I adjust the output visuals so that I can view only the relevant data (chIP), while not just simply 'ignoring' the input data (i.e. I'm assuming it's needed as a 'reference' for the chIP data points).

Thanks for any help in advance.



 -- output of sessionInfo(): 

R version 2.15.1 (2012-06-22)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8

attached base packages:
 [1] tools     stats4    splines   grid      stats     graphics  grDevices
 [8] utils     datasets  methods   base     

other attached packages:
 [1] xtable_1.7-0         survival_2.36-14     genefilter_1.38.0   
 [4] annotate_1.34.1      RSQLite_0.11.1       DBI_0.2-5           
 [7] KernSmooth_2.23-8    IRanges_1.14.4       AnnotationDbi_1.18.3
[10] mclust_4.0           Ringo_1.20.0         limma_3.12.3        
[13] RColorBrewer_1.0-5   Matrix_1.0-9         lattice_0.20-10     
[16] Biobase_2.16.0       BiocGenerics_0.2.0  

loaded via a namespace (and not attached):
[1] affy_1.34.0           affyio_1.24.0         BiocInstaller_1.4.7  
[4] preprocessCore_1.18.0 vsn_3.24.0            XML_3.9-4            
[7] zlibbioc_1.2.0       


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