Hi Darren,

You don't need to include each swath as a separate line in the sample
sheet. i.e. have 12 rows with the sentrix position as A to L. beadarray
should be able to detect that there are two swathes per array.

Hope this helps,

Mark


On Thu, Jun 6, 2013 at 9:11 AM, Darren Plant
<Darren.Plant@manchester.ac.uk>wrote:

> Dear Mark,
> Please see below for a copy of the commands i used. Unfortunately I'm
> still getting the same problem following your suggestion.
> Best wishes,
> Darren
>
> > processSwathData(inputDir = "data/9259561003", outputDir = "data/
> 9259561003", twoColour=NULL, textstring="_perBeadFile.txt",
> segmentHeight=326, segmentWidth=397, fullOutput=TRUE,
>  newTextString="_Grn.txt")
> > sampleSheetFile <- paste("data/9259561003", "/sampleSheet.csv", sep =
> "")
> > readLines(sampleSheetFile)
>  [1] "[Header],,,"                                           "Investigator
> Name,,,"
>  [3] "Project Name,RMS Whole Genome Expression Profiling,," "Experiment
> Name,,,"
>  [5] "Date,31/05/2013,,"                                     "[Data],,,"
>  [7] "Sample_Name,Sample_Group,Sentrix_ID,Sentrix_Position"
>  "RAMS06012,poor,9259561003,A-Swath1_Grn"
>  [9] "RM06012,poor,9259561003,A-Swath2_Grn"
>  "RM12038,good,9259561003,B-Swath1_Grn"
> [11] "RM12038,good,9259561003,B-Swath2_Grn"
>  "RM12001,good,9259561003,C-Swath1_Grn"
> [13] "RM12001,good,9259561003,C-Swath2_Grn"
>  "RM21004,poor,9259561003,D-Swath1_Grn"
> [15] "RM21004,poor,9259561003,D-Swath2_Grn"
>  "RM12039,poor,9259561003,E-Swath1_Grn"
> [17] "RM12039,poor,9259561003,E-Swath2_Grn"
>  "RM12016,good,9259561003,F-Swath1_Grn"
> [19] "RM12016,good,9259561003,F-Swath2_Grn"
>  "RM12032,good,9259561003,G-Swath1_Grn"
> [21] "RM12032,good,9259561003,G-Swath2_Grn"
>  "RM12041,poor,9259561003,H-Swath1_Grn"
> [23] "RM12041,poor,9259561003,H-Swath2_Grn"
>  "RM15003,poor,9259561003,I-Swath1_Grn"
> [25] "RM15003,poor,9259561003,I-Swath2_Grn"
>  "RM20020,good,9259561003,J-Swath1_Grn"
> [27] "RM20020,good,9259561003,J-Swath2_Grn"
>  "RM20022,good,9259561003,K-Swath1_Grn"
> [29] "RM20022,good,9259561003,K-Swath2_Grn"
>  "RM10025,poor,9259561003,L-Swath1_Grn"
> [31] "RM10025,poor,9259561003,L-Swath2_Grn"
>
> > data <- readIllumina("data", sampleSheet = sampleSheetFile, useImages =
> FALSE, illuminaAnnotation = "Humanv4")
> Sample Sheet D:\work\RAMS\data\9259561003\sampleSheet.csv will be used to
> read the data
> Processing section 9259561003_A-Swath1_Grn
> Processing section 9259561003_A-Swath2_Grn
> Processing section 9259561003_B-Swath1_Grn
> Processing section 9259561003_B-Swath2_Grn
> Processing section 9259561003_C-Swath1_Grn
> Processing section 9259561003_C-Swath2_Grn
> Processing section 9259561003_D-Swath1_Grn
> Processing section 9259561003_D-Swath2_Grn
> Processing section 9259561003_E-Swath1_Grn
> Processing section 9259561003_E-Swath2_Grn
> Processing section 9259561003_F-Swath1_Grn
> Processing section 9259561003_F-Swath2_Grn
> Processing section 9259561003_G-Swath1_Grn
> Processing section 9259561003_G-Swath2_Grn
> Processing section 9259561003_H-Swath1_Grn
> Processing section 9259561003_H-Swath2_Grn
> Processing section 9259561003_I-Swath1_Grn
> Processing section 9259561003_I-Swath2_Grn
> Processing section 9259561003_J-Swath1_Grn
> Processing section 9259561003_J-Swath2_Grn
> Processing section 9259561003_K-Swath1_Grn
> Processing section 9259561003_K-Swath2_Grn
> Processing section 9259561003_L-Swath1_Grn
> Processing section 9259561003_L-Swath2_Grn
>
>
> datasumm <- summarize(data,useSampleFac=T,sampleFac=rep(1:12,each=2))
> Finding list of unique probes in beadLevelData
> 48324  unique probeIDs found
> Number of unmapped probes removed:  217 Summarizing  G  channel Processing
> Array 1 Summarizing  G  channel Processing Array 2 Removing outliers Using
> exprFun Using varFun Summarizing  G  channel Processing Array 3 Summarizing
>  G  channel Processing Array 4 Removing outliers Using exprFun Using varFun
> Summarizing  G  channel Processing Array 5 Summarizing  G  channel
> Processing Array 6 Removing outliers Using exprFun Using varFun Summarizing
>  G  channel Processing Array 7 Summarizing  G  channel Processing Array 8
> Removing outliers Using exprFun Using varFun Summarizing  G  channel
> Processing Array 9 Summarizing  G  channel Processing Array 10 Removing
> outliers Using exprFun Using varFun Summarizing  G  channel Processing
> Array 11 Summarizing  G  channel Processing Array 12 Removing outliers
> Using exprFun Using varFun Summarizing  G  channel Processing Array 13
> Summarizing  G  channel Processing Array 14 Removing outliers Using exprFun
> Using varFun Summarizing  G  channel Processing Array 15 Summarizing  G
>  channel Processing Array 16 Removing outliers Using exprFun Using varFun
> Summarizing  G  channel Processing Array 17 Summarizing  G  channel
> Processing Array 18 Removing outliers Using exprFun Using varFun
> Summarizing  G  channel Processing Array 19 Summarizing  G  channel
> Processing Array 20 Removing outliers Using exprFun Using varFun
> Summarizing  G  channel Processing Array 21 Summarizing  G  channel
> Processing Array 22 Removing outliers Using exprFun Using varFun
> Summarizing  G  channel Processing Array 23 Summarizing  G  channel
> Processing Array 24 Removing outliers Using exprFun Using varFun Making
>  summary object Annotating control probes using package illuminaHumanv4.db
> Version:1.16.0
>
> Error in value[[3L]](cond) : row names supplied are of the wrong length
>   AnnotatedDataFrame 'initialize' could not update varMetadata:
>   perhaps pData and varMetadata are inconsistent?
>
>
>
>
> -----Original Message-----
> From: Mark Dunning [mailto:mark.dunning@gmail.com]
> Sent: 05 June 2013 15:45
> To: Darren Plant
> Cc: bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] beadarray - combining swath files
>
> Hi Darren,
>
> I'm having a little trouble trying to reproduce the error. What commands
> did you use to generate the bead-level data? It seems to work for the data
> that I have.
>
> In the meantime, you can force beadarray to consolidate sections by using
> the sampleFac argument. The resulting object will then have all columns
> (samples).
>
> > bsd <- summarize(bld,useSampleFac=T,sampleFac=rep(1:12,each=2))
>
> > bsd
> ExpressionSetIllumina (storageMode: list)
> assayData: 48107 features, 12 samples
>   element names: exprs, se.exprs, nObservations
> protocolData: none
> phenoData
>   rowNames: 8106854095_A 8106854095_B ... 8106854095_L (12 total)
>   varLabels: sampleID SampleFac
>   varMetadata: labelDescription
> featureData
>   featureNames: ILMN_1802380 ILMN_1893287 ... ILMN_1806862 (48107
>     total)
>   fvarLabels: ArrayAddressID IlluminaID Status
>   fvarMetadata: labelDescription
> experimentData: use 'experimentData(object)'
> Annotation: Humanv4
> QC Information
>  Available Slots:
>   QC Items: Date, Beadchip, ..., SampleGroup, numBeads
>   sampleNames: 8106854095_A-Swath1, 8106854095_A-Swath2, ...,
> 8106854095_L-Swath1, 8106854095_L-Swath2
>
> Please send me your code though.
>
> Regards,
>
> Mark
>
>
>
> On Wed, Jun 5, 2013 at 9:43 AM, Darren <darren.plant@manchester.ac.uk>
> wrote:
>
>
>         Sunitha M <sunkorner@...> writes:
>
>         >
>         > Dear all,
>         >
>         > I am trying to analyse Illumina beadarray data produced by iScan
> for the
>         first time. This scanner saves each
>         > array in two different tiff images. As a first step, I used
>         ProcessSwathData() function that
>         > deconvolutes the bead-level data and creates two files, swath1
> and
>         swath2 for the two tiff images.
>         > However, in the subsequent step, i. e. readIllumina function
> these two
>         files are treated as if they are
>         > from two different arrays (although they belong to one array).
> Is there
>         any parameter we can pass to the
>         > readIllumina function to indicate that those two files belongs
> to one
>         array.
>         >
>         > Any help in this regard is highly appreciated.
>         >
>         > Thanks
>         >
>         > Sunitha
>         >
>         >       [[alternative HTML version deleted]]
>         >
>         >
>
>         > Dear Sunitha,
>         i hope you don't mind me joining in but i am faced with the same
> problem.
>         There is no information on how to proceed with iScan data after
>         ProcessSwathData() as far as i can see. Please let me know if you
> figure
>         this out. I think others have used Illumina software to process
> the tiff
>         files as an alternative.
>         Best wishes,
>         Darren
>
>         > _______________________________________________
>         > Bioconductor mailing list
>         > Bioconductor@...
>         > https://stat.ethz.ch/mailman/listinfo/bioconductor
>         > Search the archives:
>         http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>         _______________________________________________
>         Bioconductor mailing list
>         Bioconductor@r-project.org
>         https://stat.ethz.ch/mailman/listinfo/bioconductor
>         Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>

	[[alternative HTML version deleted]]

