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

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