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.
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
Department of Genetics and Genomic Sciences
Mount Sinai School of Medicine
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