[BioC] using smoothX in Ringo

[Joern Toedling]

Hi Lizzy,

thanks for sending me these. I am still puzzled by the error message, but I
think the problem are the factor-vectors in your probeAnno PA. The "index"
components are assumed to be either character vectors that correspond to the
featureNames of X or integer vectors corresponding to row numbers in X. The
factors will mess this up quite a bit.

When you generate the data.frame before calling posToProbeAnno (which is what
you are doing I assume), you can use to the argument "stringsAsFactors=FALSE"
to suppress the default conversion of character vectors. Alternatively, you
can use the "as.character" function afterwards to convert the respective
columns of this data.frame (or components of PA) into normal character vectors.

I probably need to add a check for this situation to the respective functions.
Thanks for pointing this out.

Please let me know if you can resolve the error by not using factors in the
probeAnno object.

Cheers,
Joern

On Wed, 18 Aug 2010 15:33:11 +0100, Elizabeth Ashley wrote
> 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

---
Joern Toedling
Institut Curie -- U900
26 rue d'Ulm, 75005 Paris, FRANCE
Tel. +33 (0)156246927