[BioC] Ringo for Nimblegen ChIP-chip data in GEO

Yong Li yong.li at zbsa.uni-freiburg.de
Sun Oct 10 23:08:59 CEST 2010

Dear all,

I wanted to re-analyze a ChIP-chip dataset in GEO. Because it was from 
Nimblegen I thought Ringo is a good option. Although the raw data in GEO 
are not in the form as mentioned in the Ringo documentation, I have 
managed to read in the data with read.maimages and made a RGlist, then 
did some analysis with Ringo. However I still have a few questions.

1) I don't find any information about spot types so I didn't make any 
use of spot types. Is this a problem?

2) When I ran
 > image(rg, 1, channel="green", 
mycols=c("black","green4","springgreen")) # rg is my RGlist

I got error:
all(c(dim1, dim2) %in% names(x$genes)) is not TRUE

Could anyone explain a little more of this error?

3) The dataset consists of data for three antibodies. I am just 
interested in data for one antibody, which has two biological 
replicates. I guess it's better to include only the two samples I am 
interested in normalization (the step preprocess). Any comments?

4) In the computeRunningMedians step, because I have two replicates and 
want to combine them, I should use combineReplicates=TRUE. Am I correct?

Thanks in advance!


 > sessionInfo()
R version 2.11.1 (2010-05-31)

[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252

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

other attached packages:
  [1] biomaRt_2.4.0      Ringo_1.12.0       Matrix_0.999375-39 
  [5] limma_3.4.4        RColorBrewer_1.0-2 Biobase_2.8.0 
  [9] RCurl_1.4-2        bitops_1.0-4.1

loaded via a namespace (and not attached):
  [1] annotate_1.26.1      AnnotationDbi_1.10.2 Biostrings_2.16.9
  [4] BSgenome_1.16.5      DBI_0.2-5            genefilter_1.30.0
  [7] GenomicRanges_1.0.9  IRanges_1.6.9        KernSmooth_2.23-3
[10] RSQLite_0.9-1        splines_2.11.1       survival_2.35-8
[13] tools_2.11.1         XML_3.1-0            xtable_1.5-6

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