[BioC] Ringo for Nimblegen ChIP-chip data in GEO
yong.li at zbsa.uni-freiburg.de
Sun Oct 10 23:08:59 CEST 2010
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!
R version 2.11.1 (2010-05-31)
 LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
 LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
attached base packages:
 grid stats graphics grDevices utils datasets methods
other attached packages:
 biomaRt_2.4.0 Ringo_1.12.0 Matrix_0.999375-39
 limma_3.4.4 RColorBrewer_1.0-2 Biobase_2.8.0
 RCurl_1.4-2 bitops_1.0-4.1
loaded via a namespace (and not attached):
 annotate_1.26.1 AnnotationDbi_1.10.2 Biostrings_2.16.9
 BSgenome_1.16.5 DBI_0.2-5 genefilter_1.30.0
 GenomicRanges_1.0.9 IRanges_1.6.9 KernSmooth_2.23-3
 RSQLite_0.9-1 splines_2.11.1 survival_2.35-8
 tools_2.11.1 XML_3.1-0 xtable_1.5-6
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