[BioC] AgiMicroRna problems

[Mark Cowley]

Has anyone had success using AgiMicroRna recently? what array types were you using?
cheers,
Mark

On 21/09/2010, at 9:44 PM, Mark Cowley wrote:

> Dear Pedro, and BioCers
> similar to these 2 posts, i'm having problems running AgiMicroRna,  
> because my Agilent TXT files are missing these three columns:  
> gMeanSignal, gBGUsed, chr_coord.
> https://www.stat.math.ethz.ch/pipermail/bioconductor/2010-August/035136.html
> http://comments.gmane.org/gmane.science.biology.informatics.conductor/28101
> 
> Here was my first attempt
>> library("AgiMicroRna")
>> targets.micro=readTargets(infile="/Volumes/****/projects/****/ 
> targets.txt") (sorry - paranoid collaborator)
>> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE)
> Error in readGenericHeader(fullname, columns = columns, sep = sep) :
>   Specified column headings not found in file
> 
> I then tried to recreate my own readMicroRnaAFE which constructed  
> dummy chr_coord, BGKus objects, but then I wasn't able to run the  
> cvArray function:
>> library("AgiMicroRna")
>> targets.micro=readTargets(infile="/Volumes/external/projects/LW/ 
> targets.txt")
>> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE)
> # QC plots ran OK
>> cvArray(dd.micro,"MeanSignal",targets.micro,verbose=TRUE)
> Foreground: MeanSignal
> 
> 	FILTERING BY ControlType FLAG
> 
>  RAW DATA: 			 15739
> Error in object$other[[k]][i, , drop = FALSE] :
>   incorrect number of dimensions
>> cvArray(dd.micro,"ProcessedSignal",targets.micro,verbose=TRUE)
> Foreground: ProcessedSignal
> 
> 	FILTERING BY ControlType FLAG
> 
>  RAW DATA: 			 15739
> Error in object$other[[k]][i, , drop = FALSE] :
>   incorrect number of dimensions
> 
> I gave up on this approach, and instead I followed Pedro's advice in  
> the first URL that I mentioned, and used gTotalSignal instead of  
> gMeanSignal, and removed instances of chr_coord and gBGUsed, but then  
> I can't get TGS, or RMA normalization to work
> 
>> library("AgiMicroRna")
>> targets.micro=readTargets(infile="/Volumes/****/projects/****/ 
> targets.txt") (sorry - paranoid collaborator)
> ddaux=read.maimages(files=targets.micro$FileName,source="agilent",
> +                             
> other.columns=list(IsGeneDetected="gIsGeneDetected",
> + 
>                                                                         IsSaturated 
> ="gIsSaturated",
> + 
>                                                                         IsFeatNonUnifOF 
> ="gIsFeatNonUnifOL",
> + 
>                                                                         IsFeatPopnOL 
> ="gIsFeatPopnOL",
> + 
>                                                                         BGKmd 
> ="gBGMedianSignal"),
> +                          columns=list(Rf="gTotalGeneSignal",
> +                                                          
> Gf="gTotalProbeSignal",
> +                                                          
> Rb="gTotalGeneSignal",
> +                                                          
> Gb="gProcessedSignal"),
> +                          verbose=TRUE,sep="\t",quote="")
>> ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = T,  
> makePLOTpost = T, targets.micro, verbose = TRUE)
> Error in density.default(object[, n], na.rm = TRUE) :
>   need at least 2 points to select a bandwidth automatically
>> 
>> ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = F,  
> makePLOTpost = F, targets.micro, verbose = TRUE)
> Error in xy.coords(x, y) : 'x' and 'y' lengths differ
>> 
>> 
>> ddTGS.rma = rmaMicroRna(ddaux, normalize = TRUE, background = TRUE)
> Error in split.default(0:(length(pNList) - 1), pNList) :
>   Group length is 0 but data length > 0
> # this takes quite a few minutes to process, then gives this error
> 
> I've seen quite a bit of Agilent microRNA data through our centre, and  
> can't recall ever seeing a chr_coord column, so is this to do with  
> different versions of Agilent Feature Extraction, or different  
> defaults set by the array facility?
> 
> I'd really like to RMA normalize these data, so any help would be  
> really appreciated
> 
> cheers,
> Mark
> 
> 
> sessionInfo()
> R version 2.11.1 (2010-05-31)
> i386-apple-darwin9.8.0
> 
> locale:
> [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] AgiMicroRna_1.2.0     preprocessCore_1.10.0 affy_1.26.1            
> limma_3.4.3           Biobase_2.8.0
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0 tools_2.11.1
>> 
> 
> 
> -----------------------------------------------------
> Mark Cowley, PhD
> 
> Peter Wills Bioinformatics Centre
> Garvan Institute of Medical Research, Sydney, Australia
> -----------------------------------------------------
> 
> 
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> 
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