[BioC] beadarray - combining swath files

Darren Plant Darren.Plant at manchester.ac.uk
Thu Jun 6 14:15:07 CEST 2013


Dear Mark,
I tried this originally as i hadn't read that the sampleSheet would require modification in the documentation you provide. However, I couldn't get any data in to beadarray without changing the sample sheet (error below). Is there something fundamental that I'm doing wrong? Would it be possible for me to share a section array with you to see if you can use import/summarize at your end? Thank you for your continued support, this has been a real struggle for me.
Best wishes,
Darren 

> sampleSheetFile <- paste("data/9259561003", "/sampleSheet.csv", sep = "")
> readLines(sampleSheetFile)
 [1] "[Header],,,"                                          
 [2] "Investigator Name,James Sellu,,"                      
 [3] "Project Name,RAMS Whole Genome Expression Profiling,,"
 [4] "Experiment Name,Chip 1,,"                             
 [5] "Date,31/05/2013,,"                                    
 [6] "[Data],,,"                                            
 [7] "Sample_Name,Sample_Group,Sentrix_ID,Sentrix_Position" 
 [8] "RAMS06012,poor,9259561003,A"                          
 [9] "RAMS12038,good,9259561003,B"                          
[10] "RAMS12001,good,9259561003,C"                          
[11] "RAMS21004,poor,9259561003,D"                          
[12] "RAMS12039,poor,9259561003,E"                          
[13] "RAMS12016,good,9259561003,F"                          
[14] "RAMS12032,good,9259561003,G"                          
[15] "RAMS12041,poor,9259561003,H"                          
[16] "RAMS15003,poor,9259561003,I"                          
[17] "RAMS20020,good,9259561003,J"                          
[18] "RAMS20022,good,9259561003,K"                          
[19] "RAMS10025,poor,9259561003,L"                          

> data <- readIllumina("data", sampleSheet = sampleSheetFile, useImages = FALSE, illuminaAnnotation = "Humanv4")
Sample Sheet /home/mdehsdp4/RAMS/data/9259561003/sampleSheet.csv will be used to read the data
Data for section 9259561003_A not found
Data for section 9259561003_B not found
Data for section 9259561003_C not found
Data for section 9259561003_D not found
Data for section 9259561003_E not found
Data for section 9259561003_F not found
Data for section 9259561003_G not found
Data for section 9259561003_H not found
Data for section 9259561003_I not found
Data for section 9259561003_J not found
Data for section 9259561003_K not found
Data for section 9259561003_L not found

Error in analyseDirectory(dir = x, sectionNames = as.character(dirs[[x]]),  : 
  No data found for the specified sections 

-----Original Message-----
From: Mark Dunning [mailto:mark.dunning at gmail.com] 
Sent: 06 June 2013 13:02
To: Darren Plant
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] beadarray - combining swath files

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 at 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 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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