Re: unable to set sampleNames after combine (from beadarray package) on ExpressionSetIllumina

Thanks for easily reproduced bug report Adai and the neat solution Martin.
 This has been fixed in beadarray version 2.15.4.

Mike

On 11 September 2014 12:17, Adaikalavan Ramasamy <
[email protected]> wrote:

> That's great. Thanks for sending the solution.
>
> On Wed, Sep 10, 2014 at 8:45 PM, Martin Morgan <[email protected]> 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
> >>
> >>         [[alternative HTML version deleted]]
> >>
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> >>
> >>
> >
> > --
> > Computational Biology / Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N.
> > PO Box 19024 Seattle, WA 98109
> >
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> >
>
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>
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-- 
Mike Smith
Research Associate
Statistics & Computational Biology Laboratory
Cambridge University

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