[BioC] using smoothX in Ringo

[Elizabeth Ashley]

Hi Joern

Thanks for your help so far, I've tried your suggestions and below are the outputs:

> str(X$Cy5)
 chr [1:3] "MB_C_3" "MB_E_2" ""
> validObject(PA)
[1] TRUE
> str(PA["2L.start"])
 int [1:389633] 5131 5176 5236 5281 5401 5461 5501 5571 5611 5681 ...
> str(PA["2L.index"])
 Factor w/ 2157868 levels "CHR02LFS000005131",..: 1 2 3 4 5 6 7 8 9 10 ...
> str(featureNames(X))
 chr [1:2173626] "RANDOM00060002" "RANDOM00060003" "RANDOM00060004" ...

So from what this tells me my files do not correspond correctly, can you suggest how to help them link up?

thanks again
Lizzy
________________________________________
From: Joern Toedling [Joern.Toedling at curie.fr]
Sent: 06 August 2010 10:47
To: Elizabeth Ashley; Bioconductor
Subject: Re: [BioC] using smoothX in Ringo

Hi Lizzy,

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
str(X$Cy5)
Alternatively, the probeAnno could be the culprit. What are the results of
validObject(PA)
str(PA['2L.start'])
str(PA['2L.index']) # should correspond to featureNames in X
str(featureNames(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.

Regards,
Joern



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)
> x86_64-unknown-linux-gnu
>
> locale:
>  [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
> [11] LC_MEASUREMENT=en_GB.ISO-8859-1 LC_IDENTIFICATION=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
> Lizzy
>
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---
Joern Toedling
Institut Curie -- U900
26 rue d'Ulm, 75005 Paris, FRANCE
Tel. +33 (0)156246927