[BioC] using smoothX in Ringo
Joern.Toedling at curie.fr
Fri Aug 6 11:47:54 CEST 2010
I think you are right and there might be a small issue with the objects that
you created. How exactly did you create them?
First check if the argument 'modColumn' is set correctly.
What is the output of
Alternatively, the probeAnno could be the culprit. What are the results of
str(PA['2L.index']) # should correspond to featureNames in X
Sorry that I cannot give more precise help at the moment, but I hope we can
find the problem with the information requested above.
On Thu, 5 Aug 2010 15:34:39 +0100, Elizabeth Ashley wrote
> 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:
> > smoothX<-computeRunningMedians(X,PA,modColumn="Cy5",
> + allChr="2L",winHalfSize=400)
> 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.
> > sessionInfo()
> 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
>  base
> 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
>  xtable_1.5-6
> 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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