[BioC] Analysis of chIP-chip

Joern Toedling j.toedling at imb-mainz.de
Wed Oct 17 13:57:47 CEST 2012


assuming that you are talking about the Ringo package, I am not sure 
which parts of the vignette you modified for your own data, but 
apparently you have been missing a step. In general, the data of ChIP 
and Input channel are read in, stored as an object of class RGList and 
then the function "preprocess" obtains some form of probe-wise 
fold-changes ChIP/input. This step is what you call "taking the input 
into account" and from that point on, in the vignette ChIP and Input are 
not considered separately any longer. This step results in an object of 
class ExpressionSet holding informative values for all probes. Of 
course, you can obtain such an ExpressionSet in other ways. In the 
vignette, this is followed up by a smoothing step of the fold-changes.

So my first guess would be that you omitted the call of "preprocess" and 
directly went on to the smoothing. And then of course, you still have 
ChIP and Input intensities separately.


On 10/16/2012 01:47 PM, John H [guest] wrote:
> 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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Joern Toedling, PhD
Core Facility Bioinformatics
Institute of Molecular Biology gGmbH (IMB)
Tel.: +49 6131 39 21528

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