[BioC] using smoothX in Ringo
elizabeth.ashley at linacre.ox.ac.uk
Thu Aug 5 16:34:39 CEST 2010
I am trying to use Ringo to analyse my data and am struggling with using the smoothX script, this is the script and error I get when I try to use it:
Chromosome 2L ...
MB_C_3_vs_MB_E_3 ... Error in seq.default(1, nrow(slidingRes) + 1 - length(modSamples), by = length(modSamples)) :
wrong sign in 'by' argument
In addition: Warning message:
In computeRunningMedians(X, PA, modColumn = "Cy5", allChr = "2L", :
389633 probes on chromosome 2L are listed in PA , but do not correspond to features of X .
#where PA is probe anno object.
R version 2.11.1 (2010-05-31)
 LC_CTYPE=en_GB.ISO-8859-1 LC_NUMERIC=C
 LC_TIME=en_GB.ISO-8859-1 LC_COLLATE=en_GB.ISO-8859-1
 LC_MONETARY=C LC_MESSAGES=en_GB.ISO-8859-1
 LC_PAPER=en_GB.ISO-8859-1 LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_GB.ISO-8859-1 LC_IDENTIFICATION=C
attached base packages:
 grid stats graphics grDevices utils datasets methods
other attached packages:
 biomaRt_2.4.0 Ringo_1.12.0 Matrix_0.999375-40 lattice_0.18-8
 limma_3.4.3 RColorBrewer_1.0-2 Biobase_2.8.0
loaded via a namespace (and not attached):
 affy_1.26.1 affyio_1.16.0 annotate_1.26.0
 AnnotationDbi_1.10.1 DBI_0.2-5 genefilter_1.30.0
 KernSmooth_2.23-3 preprocessCore_1.10.0 RCurl_1.4-2
 RSQLite_0.9-1 splines_2.11.1 survival_2.35-8
 tools_2.11.1 vsn_3.16.0 XML_3.1-0
no traceback available
I am particularly loooking for help with the first part of the error - but would welcome advise on the second part if you can help, though i suspect this is to do with how i created PA and X.
thanks in advance
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