[BioC] AgiMicroRna problems
Segal, Corrinne
c.segal08 at imperial.ac.uk
Thu Sep 30 15:57:24 CEST 2010
Hi,
If the data is extracted with the FE report set to 'Full' rather than 'Compact', then it reports the gMeanSignal and gBGUsed (but not chr_coord). You can then follow the package using the amendments Pedro posted to get around not having the chr_coord column.
Cheers,
Corrinne
-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of David Ruau
Sent: 29 September 2010 19:02
To: Mark Cowley
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] AgiMicroRna problems
Hi Mark,
I just received a data set of Human miRNA V3 and AgiMicroRna does not work.
Basically the column gMeanSignal, gBGUsed, chr_coord are not present.
I modified readMicroRnaAFE accordingly to the post of Pedro (see after the text)
My question is why those columns are not present in the txt file.
In the folder I received from our facility there is a XML file containing the settings of the FeatureExtraction software. One flag is TextOutPkgType="Compact"
Is there a way to test if this option can be change and what is the effect on the txt output?
readMicroRnaAFE <- function (targets, verbose = FALSE)
{
if (!is(targets, "data.frame")) {
stop("'targets' must be a data.frame")
}
ddaux=read.maimages(files=targets$FileName,source="agilent",
other.columns=list(IsGeneDetected="gIsGeneDetected",
IsSaturated ="gIsSaturated", IsFeatNonUnifOF ="gIsFeatNonUnifOL",
IsFeatPopnOL ="gIsFeatPopnOL", BGKmd ="gBGMedianSignal"),
columns=list(R="gTotalGeneSignal", G="gTotalProbeSignal",
Rb="gTotalGeneSignal", Gb="gProcessedSignal"),
verbose=TRUE,sep="\t",quote=""
)
#return(ddaux)
dd = new("RGList")
dd$R = ddaux$R
dd$G = ddaux$G
dd$Rb = ddaux$Rb
dd$Gb = ddaux$Gb
dd$targets = ddaux$targets
## suppress column 6 that should have contain chr_pos I guess
dd$genes = ddaux$genes[, c(4, 5)]
dd$other = ddaux$other
rm(ddaux)
if (verbose) {
cat("", "\n")
cat(" RGList:", "\n")
cat("\tdd$R:\t\t'gTotalGeneSignal' ", "\n")
cat("\tdd$G:\t\t'gTotalProbeSignal' ", "\n")
cat("\tdd$Rb:\t\t'gMeanSignal' ", "\n")
cat("\tdd$Gb:\t\t'gProcessedSignal' ", "\n")
cat("", "\n")
}
return(dd)
}
David
On Sep 28, 2010, at 11:52 PM, Mark Cowley wrote:
> Has anyone had success using AgiMicroRna recently? what array types were you using?
> cheers,
> Mark
>
> On 21/09/2010, at 9:44 PM, Mark Cowley wrote:
>
>> Dear Pedro, and BioCers
>> similar to these 2 posts, i'm having problems running AgiMicroRna,
>> because my Agilent TXT files are missing these three columns:
>> gMeanSignal, gBGUsed, chr_coord.
>> https://www.stat.math.ethz.ch/pipermail/bioconductor/2010-August/035136.html
>> http://comments.gmane.org/gmane.science.biology.informatics.conductor/28101
>>
>> Here was my first attempt
>>> library("AgiMicroRna")
>>> targets.micro=readTargets(infile="/Volumes/****/projects/****/
>> targets.txt") (sorry - paranoid collaborator)
>>> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE)
>> Error in readGenericHeader(fullname, columns = columns, sep = sep) :
>> Specified column headings not found in file
>>
>> I then tried to recreate my own readMicroRnaAFE which constructed
>> dummy chr_coord, BGKus objects, but then I wasn't able to run the
>> cvArray function:
>>> library("AgiMicroRna")
>>> targets.micro=readTargets(infile="/Volumes/external/projects/LW/
>> targets.txt")
>>> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE)
>> # QC plots ran OK
>>> cvArray(dd.micro,"MeanSignal",targets.micro,verbose=TRUE)
>> Foreground: MeanSignal
>>
>> FILTERING BY ControlType FLAG
>>
>> RAW DATA: 15739
>> Error in object$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
>> -----------------------------------------------------
>>
>>
>> [[alternative HTML version deleted]]
>>
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>
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