On Jul 1, 2012, at 6:15 AM, Rui Barradas wrote:
Hello,
That error is because your datum is of a class that merge.default
cannot handle, like the error message says. By the look of it, class
"TillingFeatureSet" has a print method written to print it. This
because it prints objects of that class with some descriptive
information not part of the object itself. The underlying structure
seems to be a list, which was subclassed to a "TillingFeatureSet"
class object, with methods specially written for it.
Actually the error was from the coercion function
`as.data.frame.default`. This rawData object appears to be a list of
two S4 objects, (but that is a guess) and I suspect it was created by
a BioConductor package. It's not surprising that a complex irregular
object would not have an "as" method. (None of the requested
information about the package being used (very possibly "oligo") or
other system details were provided.)
The question should probably be reformulated with more details and
sent to the BioConductor mailing list.
--
David.
Bottom line: if you merge the two components, the special behavior
that comes with its class might be lost. Do you really need to merge
them?
If so, use dput(rawData), its output, to post your object. But think
about it first.
Hope this helps,
Rui Barradas
Em 28-06-2012 16:47, Seungyeul Yoo escreveu:
Hello,
I'm wondering how I can merge two featuresets into one.
My dataset is two sets of microarray data and it looks like
followings:
rawData
$v1
TilingFeatureSet (storageMode: lockedEnvironment)
assayData: 2197815 features, 59 samples
element names: channel1, channel2
protocolData
rowNames: LT290677RU_D1_2011-02-16 LT286300LU_D1_2010-07-24 ...
LT003990RU_D1_2010-11-04 (59 total)
varLabels: filenamesChannel1 filenamesChannel2 dates1 dates2
varMetadata: labelDescription channel
phenoData
rowNames: LT290677RU_D1_2011-02-16 LT286300LU_D1_2010-07-24 ...
LT003990RU_D1_2010-11-04 (59 total)
varLabels: sampleID tissue ... Annotation (5 total)
varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.feinberg.hg18.me.hx1
$v1.1
TilingFeatureSet (storageMode: lockedEnvironment)
assayData: 2197815 features, 17 samples
element names: channel1, channel2
protocolData
rowNames: LT282562RM_D1_2010-11-22 LT280646RU_D1_2010-11-22 ...
LT093297LU_D1_2010-11-12 (17 total)
varLabels: filenamesChannel1 filenamesChannel2 dates1 dates2
varMetadata: labelDescription channel
phenoData
rowNames: LT282562RM_D1_2010-11-22 LT280646RU_D1_2010-11-22 ...
LT093297LU_D1_2010-11-12 (17 total)
varLabels: sampleID tissue ... Annotation (5 total)
varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.feinberg.hg18.me.hx1
I want to merge rawData$v1 and rawData$v1.1 since they are
consistent each other.
I was trying to use "merge" function as merge(rawData$v1, rawData
$v1.1) but it failed with error as
Error in as.data.frame.default(x) :
cannot coerce class 'structure("TilingFeatureSet", package =
"oligoClasses")' into a data.frame
Calls: merge ... merge.default -> merge -> as.data.frame ->
as.data.frame.default
Can you please help with some advices?
Thanks,
Best regards,
Seungyeul Yoo
Postdoc Fellow,
Institute of Genomics and Multiscale Biology
David Winsemius, MD
West Hartford, CT
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