[BioC] beadarray - combining swath files

Darren Plant Darren.Plant at manchester.ac.uk
Thu Jun 6 10:11:14 CEST 2013


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 at gmail.com] 
Sent: 05 June 2013 15:45
To: Darren Plant
Cc: bioconductor at 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 at manchester.ac.uk> wrote:


	Sunitha M <sunkorner at ...> 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
	
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