[BioC] using smoothX in Ringo

Elizabeth Ashley 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:

> 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)

 [1] LC_CTYPE=en_GB.ISO-8859-1       LC_NUMERIC=C
 [3] LC_TIME=en_GB.ISO-8859-1        LC_COLLATE=en_GB.ISO-8859-1
 [5] LC_MONETARY=C                   LC_MESSAGES=en_GB.ISO-8859-1
 [7] LC_PAPER=en_GB.ISO-8859-1       LC_NAME=C
 [9] LC_ADDRESS=C                    LC_TELEPHONE=C

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_0.999375-40 lattice_0.18-8
[5] limma_3.4.3        RColorBrewer_1.0-2 Biobase_2.8.0

loaded via a namespace (and not attached):
 [1] affy_1.26.1           affyio_1.16.0         annotate_1.26.0
 [4] AnnotationDbi_1.10.1  DBI_0.2-5             genefilter_1.30.0
 [7] KernSmooth_2.23-3     preprocessCore_1.10.0 RCurl_1.4-2
[10] RSQLite_0.9-1         splines_2.11.1        survival_2.35-8
[13] tools_2.11.1          vsn_3.16.0            XML_3.1-0
[16] 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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