[BioC] unable to set sampleNames after combine (from beadarray package) on ExpressionSetIllumina

[Adaikalavan Ramasamy]

That's great. Thanks for sending the solution.

On Wed, Sep 10, 2014 at 8:45 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:

> Hi Adai --
>
>
> On 09/09/2014 03:52 AM, Adaikalavan Ramasamy wrote:
>
>> Dear all,
>>
>> Here is a possible bug in the combine() function from beadarray. I read
>> two
>> ExpressionSetIllumina objects with 36 samples and 12 samples each. The
>> combine() function works brilliantly and without errors or warnings but I
>> get error message when I try to change the sample names.
>>
>> ## create fake data to read in ##
>> tmp <- data.frame( PROBE_ID = paste0("P", 1:10), SYMBOL   = LETTERS[1:10],
>>                     S1.AVG_Signal = rnorm(10, mean=7), S2.AVG_Signal =
>> rnorm(10, mean=8), S3.AVG_Signal = rnorm(10, mean=6) )
>> write.table(tmp, file="SampleProbeProfile_1.txt", sep="\t", quote=F,
>> row.names=F)
>> rm(tmp)
>>
>> tmp <- data.frame( PROBE_ID = paste0("P", 1:10), SYMBOL   = LETTERS[1:10],
>>                     S4.AVG_Signal = rnorm(10, mean=9), S5.AVG_Signal =
>> rnorm(10, mean=6) )
>> write.table(tmp, file="SampleProbeProfile_2.txt", sep="\t", quote=F,
>> row.names=F)
>> rm(tmp)
>>
>>
>> ## Read in and combine ##
>> raw1 <- readBeadSummaryData(dataFile="SampleProbeProfile_1.txt",
>> ProbeID="PROBE_ID", columns=list(exprs="AVG_Signal"), skip=0)
>> raw2 <- readBeadSummaryData(dataFile="SampleProbeProfile_2.txt",
>> ProbeID="PROBE_ID", columns=list(exprs="AVG_Signal"), skip=0)
>>
>> raw  <- combine(raw1, raw2)  # no warnings or error
>>
>> dim(raw1)
>> # Features  Samples Channels
>> #       10        3        1
>>
>> dim(raw2)
>> # Features  Samples Channels
>> #      10        2        1
>>
>> dim(raw)
>> # Features  Samples Channels
>> #       10        5        1
>>
>> raw1, raw2 and raw are all of ExpressionSetIllumina class.
>>
>>
>> And here is the problem:
>>
>> sampleNames(raw) <- paste0("Sample", 1:5)
>> # Error in `sampleNames<-`(`*tmp*`, value = c("Sample1", "Sample2",
>> "Sample3",  :
>> #  number of new names (5) should equal number of rows in
>>
>
> the problem is that beadarray does not 'combine' the 'protocolData' slot
> and does not check that the resulting object is valid
>
> > validObject(raw)
> Error in validObject(raw) :
>   invalid class "ExpressionSetIllumina" object: 1: sample numbers differ
> between phenoData and protocolData
> invalid class "ExpressionSetIllumina" object: 2: sampleNames differ
> between phenoData and protocolData
>
> A work-around is to update the protocolData slot yourself, until the
> package maintainer (cc'd) has a chance to fix the problem.
>
> > protocolData(raw) <- combine(protocolData(raw1), protocolData(raw2))
> > validObject(raw)
> [1] TRUE
> > sampleNames(raw) <- 1:5
> >
>
> Thanks for the nice reproducible example
>
> Martin
>
>  AnnotatedDataFrame (3)
>>
>>
>> Alternatively, I could change the rownames of raw1 and raw2 separately and
>> then combine but I am just curious as to why this error message. Thank
>> you.
>>
>> Regards, Adai
>>
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>>
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>>
>
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