[R] Merging listed dataset into one

[Rui Barradas]

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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