[BioC] AgiMicroRna problems
Mark Cowley
m.cowley at garvan.org.au
Thu Sep 30 16:46:53 CEST 2010
Hi,
I wonder if our core facility even knows about that option!
Thanks for bringing this up
cheers,
mark
On 30/09/2010, at 11:57 PM, Segal, Corrinne wrote:
> 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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