[BioC] DEXSeq Help Needed: newExonCountSet() error messages

[Wolfgang Huber]

Margaret

You will need something similar to:

 newExonCountSet(countData = data[, relevant.columns], design=samples,
        geneIDs=data$geneID, exonIDs=data$exonID)

but the exact wording depends on the details of your data. In your post, you were trying to apply functions 'counts', 'design' etc. on data frames, for which they are not defined. Have a look at the instructions in the manual page of "newExonCountSet", some think they are pretty clear, but please let us know if you find something missing. 
To use DEXSeq, it is necessary to have a basic familiarity with basic R concepts such as "data frame", "matrix", "factor" etc., have a look at the "Introduction to R" that comes with R. 

Best wishes
	Wolfgang




>> newExonCountSet(countData=counts(data), design=design(samples),
> geneIDs=geneIDs(data), exonIDs=exonIDs(data))


On Jul 5, 2013, at 6:02 pm, Margaret Linan <mlinan at asu.edu> wrote:

> Hi,
> 
> I attempted to use the DEXSeq function newExonCountSet() and received this
> error message:
> 
>> newExonCountSet(countData=counts(data), design=design(samples),
> geneIDs=geneIDs(data), exonIDs=exonIDs(data))
> 
> * Error in (function (classes, fdef, mtable)  :
>  unable to find an inherited method for function ‘counts’ for signature
> ‘"data.frame"’*
> 
> The object "data" was created with a read.Table() function in Windows R
> 3.0.1, and is similar to the modified pasilla example pasted below.
> 
> gene_id untreated1 untreated2 untreated3 untreated4 treated1 treated2
> treated3
> 
> FBgn0000003:1 0 0 0 0 1 2 3
> 
> FBgn0000003:2 0 0 0 0 7 8 9
> 
> FBgn0000008:1 92 161 76 70 140 88 70
> 
> FBgn0000008:2 5 1 1 0 4 5 6
> 
> FBgn0000011+FBgn00000304:2 5 1 0 0 4 0 0
> 
> FBgn0000015:1 0 2 1 2 9 10 11
> 
> FBgn0000015:2 4664 8714 3564 3150 6205 3072 2222
> 
> FBgn0000015:3 583 761 222 310 722 299 111
> 
> What does the error message mean and should I change anything in particular
> to avoid the error message?
> 
> I am especially confused because the newExonCountSet function is meant to
> work with a data.frame, and yet
> 
> the error messages says there is no function available to process the
> data.frame.
> 
> Here is some output from separately run portions of the newExonCountSet:
> 
> 
> 
>> counts(data)
> Error in (function (classes, fdef, mtable)  :
>  unable to find an inherited method for function ‘counts’ for signature
> ‘"data.frame"’
> 
>> design(samples)
> Error in (function (classes, fdef, mtable)  :
>  unable to find an inherited method for function ‘design’ for signature
> ‘"data.frame"’
> 
> Note: The object "samples" had no errors when I created it. I used
> head(samples,4) to check it out.
> 
>> exonIDs(data)
> Error: is(ecs, "ExonCountSet") is not TRUE
> 
> 
> 
>> geneIDs(data)
> Error: is(ecs, "ExonCountSet") is not TRUE
> 
> 
> 
> I really appreciate anyone helping me resolve these errors.
> 
> Here is the sessionInfo()
> 
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> 
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252
> LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
> 
> other attached packages:
> [1] DESeq_1.12.0       lattice_0.20-15    locfit_1.5-9.1
> DEXSeq_1.6.0       Biobase_2.20.0     BiocGenerics_0.6.0
> 
> loaded via a namespace (and not attached):
> [1] annotate_1.38.0      AnnotationDbi_1.22.5 biomaRt_2.16.0
> Biostrings_2.28.0    bitops_1.0-5         DBI_0.2-7
> genefilter_1.42.0
> [8] geneplotter_1.38.0   GenomicRanges_1.12.4 grid_3.0.1
> hwriter_1.3          IRanges_1.18.1       RColorBrewer_1.0-5
> RCurl_1.95-4.1
> [15] Rsamtools_1.12.3     RSQLite_0.11.4       splines_3.0.1
> statmod_1.4.17       stats4_3.0.1         stringr_0.6.2
> survival_2.37-4
> [22] tools_3.0.1          XML_3.96-1.1         xtable_1.7-1
> zlibbioc_1.6.0
> 
> 
> 
> Thanks,
> 
> Margaret Linan
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor