[BioC] AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828.
Richard Friedman
friedman at cancercenter.columbia.edu
Wed Jun 30 21:36:59 CEST 2010
Pedro,
I just got back to the microRNA today.
Thank you very much!
Best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/
In Memoriam,
George Scithers
On Jun 21, 2010, at 5:04 AM, Pedro López Romero wrote:
> Hi Neel and Richard,
>
> Thanks for your patience.
>
>
>
> I have slitghtly modified some code in the package, basically
> related to the way read.maimages is used. I have eliminated the use
> of the "chr_coord" column in some of the output files which it was
> what it was causing problems. Before these changes are made
> effective in the library, please, try this temporal solution:
>
>
>
> dd=read.maimages(files=targets$FileName,source="agilent",
>
> columns=list(Rf="gTotalGeneSignal",
>
>
> Gf="gTotalProbeSignal",
>
>
> Rb="gMeanSignal",
>
>
> Gb="gProcessedSignal"),
>
>
> other.columns=list(IsGeneDetected="gIsGeneDetected",
>
> IsSaturated
> ="gIsSaturated",
>
> IsFeatNonUnifOF
> ="gIsFeatNonUnifOL",
>
> IsFeatPopnOL
> ="gIsFeatPopnOL",
>
>
> probe_mappings="probe_mappings",
>
> BGKmd
> ="gBGMedianSignal",
>
> BGKus
> ="gBGUsed"),
>
> annotation = c( "ControlType",
> "ProbeName","GeneName"),
>
> verbose=TRUE,sep="\t",quote="")
>
>
>
>
>
> before doing anything else, please check first that you have
> "probe_mappings" in the fifth position of "dd$other"
>
>> names(dd$other)[5]
>
> [1] "probe_mappings"
>
>
>
> Then, change the name of "probe_mappings" to the name that
> AgiMicroRna uses for this variable:
>
>> names(dd$other)[5] = "chr_coord"
>
>
>
> Then, use the rest of the functions as usual:
>
>
>
> ddTGS.rma = rmaMicroRna(dd, normalize = TRUE, background = FALSE)
>
> ddPROC = filterMicroRna(ddTGS.rma,
>
> dd,
>
> control = TRUE,
>
> IsGeneDetected = TRUE,
>
> wellaboveNEG = FALSE,
>
> limIsGeneDetected = 50,
>
> limNEG = 25,
>
> makePLOT = FALSE,
>
> targets,
>
> verbose = TRUE)
>
>
>
>
>
> Please, let me know if you still have any problem. Thanks
>
>
>
> p.-
>
>
>
>
>
> De: Neel Aluru [mailto:naluru at whoi.edu]
> Enviado el: Friday, June 18, 2010 1:44 PM
> Para: Pedro López Romero; bio c bioconductor
> Asunto: RE: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse
> miRNA Microarray Release 12.0 G4471A-021828.
>
>
>
> Thanks, Pedro. Looking forward to hearing from you.
>
> Sincerely,
> Neel
>
> At 03:20 AM 6/18/2010, Pedro López Romero wrote:
>
>
>
> Thanks Neel,
>
> I am working on your data, I know where the problem is. I have to
> modify (or even write a new function) to read the data in such a
> way that it is more flexible to the different data formats. I will
> let you know when I have this ready.
>
> p.-
>
> De: Neel Aluru [ mailto:naluru at whoi.edu <mailto:naluru at whoi.edu> ]
> Enviado el: Thursday, June 17, 2010 1:49 PM
> Para: Pedro López Romero; bio c bioconductor
> Asunto: RE: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse
> miRNA Microarray Release 12.0 G4471A-021828.
>
> Thanks, Pedro.
>
> Here are the details you. I have noticed that what is in dd$genes
> and dd$other is different depending on whether I use read.maimages
> or readMicroRnaAFE function. I have pasted the details from both of
> them.
>
> The feature extraction software I used was version 9.3.
>
> Sincerely,
> Neel
>
> Session info () using read.maimages function
>
>> library("AgiMicroRna")
>> targets.micro=readTargets(infile="targets.txt", verbose=TRUE)
>
> Target File
> FileName Treatment GErep Subject
> 36_DMSO_1 36_DMSO_1.txt 36DMSO 1 1
> 36_DMSO_2 36_DMSO_2.txt 36DMSO 1 2
> 36_DMSO_3 36_DMSO_3.txt 36DMSO 1 3
> 36_TCDD_1 36_TCDD_1.txt 36TCDD 2 1
> 36_TCDD_2 36_TCDD_2.txt 36TCDD 2 2
> 36_TCDD_3 36_TCDD_3.txt 36TCDD 2 3
> 60_DMSO_1 60_DMSO_1.txt 60DMSO 3 1
> 60_DMSO_2 60_DMSO_2.txt 60DMSO 3 2
> 60_DMSO_3 60_DMSO_3.txt 60DMSO 3 3
> 60_TCDD_1 60_TCDD_1.txt 60TCDD 4 1
> 60_TCDD_2 60_TCDD_2.txt 60TCDD 4 2
> 60_TCDD_3 60_TCDD_3.txt 60TCDD 4 3
>
>> ddaux=read.maimages(files=targets.micro$FileName,source="agilent",
> + other.columns=list(IsGeneDetected="gIsGeneDetected",
> + IsSaturated="gIsSaturated",
> + IsFeatNonUnifOF="gIsFeatNonUnifOL",
> + IsFeatPopnOL="gIsFeatPopnOL",
> + ChrCoord="chr_coord", BGKmd="gBGMedianSignal",
> + BGKus="gBGUsed"),
> + columns=list(Rf="gTotalGeneSignal",
> + Gf="gTotalProbeSignal",
> + Rb="gMeanSignal",Gb="gProcessedSignal"),
> verbose=TRUE,sep="\t",quote="")
> Read 36_DMSO_1.txt
> Read 36_DMSO_2.txt
> Read 36_DMSO_3.txt
> Read 36_TCDD_1.txt
> Read 36_TCDD_2.txt
> Read 36_TCDD_3.txt
> Read 60_DMSO_1.txt
> Read 60_DMSO_2.txt
> Read 60_DMSO_3.txt
> Read 60_TCDD_1.txt
> Read 60_TCDD_2.txt
> Read 60_TCDD_3.txt
>> names(ddaux)
> [1] "R" "G" "Rb" "Gb" "targets" "genes"
> "source"
> [8] "other"
>> names(ddaux$genes)
> [1] "Row" "Col" "Start" "Sequence"
> [5] "ProbeUID" "ControlType" "ProbeName" "GeneName"
> [9] "SystematicName" "Description"
>> names(ddaux$other)
> [1] "gIsGeneDetected" "gIsSaturated" "gIsFeatNonUnifOL"
> "gIsFeatPopnOL"
> [5] "gBGMedianSignal" "gBGUsed"
>
> Session Info () with AgiMicroRnaAFE function.
>
>> ddaux=readAgiMicroRnaAFE(targets.micro, verbose=TRUE)
> Error: could not find function "readAgiMicroRnaAFE"
>> ddaux=readMicroRnaAFE(targets.micro, verbose=TRUE)
> Read 36_DMSO_1.txt
> Read 36_DMSO_2.txt
> Read 36_DMSO_3.txt
> Read 36_TCDD_1.txt
> Read 36_TCDD_2.txt
> Read 36_TCDD_3.txt
> Read 60_DMSO_1.txt
> Read 60_DMSO_2.txt
> Read 60_DMSO_3.txt
> Read 60_TCDD_1.txt
> Read 60_TCDD_2.txt
> Read 60_TCDD_3.txt
>
> RGList:
> dd$R: 'gTotalGeneSignal'
> dd$G: 'gTotalProbeSignal'
> dd$Rb: 'gMeanSignal'
> dd$Gb: 'gProcessedSignal'
>
>> names(ddaux)
> [1] "R" "G" "Rb" "Gb" "targets" "genes"
> "other"
>> names(ddaux$genes)
> [1] "Sequence" "ProbeUID" "ControlType"
>> names(ddaux$other)
> [1] "gIsGeneDetected" "gIsSaturated" "gIsFeatNonUnifOL"
> "gIsFeatPopnOL"
> [5] "gBGMedianSignal" "gBGUsed"
>
>
>
> At 04:29 AM 6/17/2010, Pedro López Romero wrote:
>
> Hi Neel,
>
> I think your problem with the filtering function, is not the
> filtering itself but when the function tries to write an output. I
> am modifying this, so the user can choose whether or not they want
> to have an output file in the filtering step. In the meantime, can
> you tell me what you have in?
> names(dd),
> names(dd$genes)
> names(dd$genes)
> names(dd$other)
>
> What version of the Extractor are you using?
>
>
>
> p.-
>
> De: Neel Aluru [ <mailto:naluru at whoi.edu> mailto:naluru at whoi.edu]
> Enviado el: Wednesday, June 16, 2010 10:54 PM
> Para: Richard Friedman; Pedro López Romero; bio c bioconductor
> Asunto: Re: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse
> miRNA Microarray Release 12.0 G4471A-021828.
>
> Hi Rich,
>
> Did you try filtering probes using FilterMicroRna function after
> removing the two columns. I am having difficulty in filtering probes.
>
> Thanks,
> Neel
>
> At 04:19 PM 6/16/2010, Richard Friedman wrote:
>
> Dear Pedro and List,
>
> My text files form Agilent Mouse miRNA Microarray Release 12.0
> G4471A-021828 has two extra columns which are not
> in GSE19232 Agilent human microRNA array v 2.0 (G44708) - "start"
> and "sequence". When these are deleted
> AgiMicroRNA works. I do not know if this is due to the array or
> software or processing options on the software.
> This clears up the problem with maMicroRna( which i have been writing
> you about. It would be nice if
> this could be taken into automatically in a future version of
> AgiMicroRNA, but this solves my porblem for now.
>
> Thanks and best wishes,
> Rich
> ------------------------------------------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist,
> Biomedical Informatics Shared Resource
> Herbert Irving Comprehensive Cancer Center (HICCC)
> Lecturer,
> Department of Biomedical Informatics (DBMI)
> Educational Coordinator,
> Center for Computational Biology and Bioinformatics (C2B2)/
> National Center for Multiscale Analysis of Genomic Networks (MAGNet)
> Room 824
> Irving Cancer Research Center
> Columbia University
> 1130 St. Nicholas Ave
> New York, NY 10032
> (212)851-4765 (voice)
> friedman at cancercenter.columbia.edu
> http://cancercenter.columbia.edu/~friedman/
>
> In Memoriam,
> George Scithers
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> Neel Aluru Ph.D.
> Post doctoral Scholar
> Biology Department
> Redfield 304 (MS#32)
> Woods Hole Oceanographic Institution
> Woods Hole MA 02543 USA
> Phone: (508) 289-3607 [Office]
> 774-392-3727 [Cell]
> RID: A-7237-2009
>
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> Post doctoral Scholar
> Biology Department
> Redfield 304 (MS#32)
> Woods Hole Oceanographic Institution
> Woods Hole MA 02543 USA
> Phone: (508) 289-3607 [Office]
> 774-392-3727 [Cell]
> RID: A-7237-2009
>
> ________________________________
>
> *************** AVISO LEGAL ***************
> Este mensaje va dirigido, de manera exclusiva, a su destinatario y
> contiene información confidencial y sujeta al secreto profesional,
> cuya divulgación no está permitida por la ley. En caso de haber
> recibido este mensaje por error, le rogamos que, de forma inmediata,
> nos lo comunique mediante correo electrónico remitido a nuestra
> atención o a través del teléfono (+34 914531200) y proceda a su
> eliminación, así como a la de cualquier documento adjunto al mismo.
> Asimismo, le comunicamos que la distribución, copia o utilización de
> este mensaje, o de cualquier documento adjunto al mismo, cualquiera
> que fuera su finalidad, están prohibidas por la ley. Le informamos,
> como destinatario de este mensaje, que el correo electrónico y las
> comunicaciones por medio de Internet no permiten asegurar ni
> garantizar la confidencialidad de los mensajes transmitidos, así
> como tampoco su integridad o su correcta recepción, por lo que el
> CNIC no asume responsabilidad alguna por tales circunstancias. Si no
> consintiese la utilización del correo electrónico o de las
> comunicaciones vía Internet le rogamos nos lo comunique y ponga en
> nuestro conocimiento de manera inmediata.
>
> ________________________________
>
> *************** LEGAL NOTICE **************
> This message is intended exclusively for the person to whom it is
> addressed and contains privileged and confidential information
> protected from disclosure by law. If you are not the addressee
> indicated in this message, you should immediately delete it and any
> attachments and notify the sender by reply e-mail or by phone (+34
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> assume any liability for those circumstances. Should you not agree
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> kindly requested to notify us immediately.
>
> Neel Aluru Ph.D.
> Post doctoral Scholar
> Biology Department
> Redfield 304 (MS#32)
> Woods Hole Oceanographic Institution
> Woods Hole MA 02543 USA
> Phone: (508) 289-3607 [Office]
> 774-392-3727 [Cell]
> RID: A-7237-2009
>
>
>
>
> *************** AVISO LEGAL ***************
>
> Este mensaje va dirigido, de manera exclusiva, a su destinatario y
>
> contiene información confidencial y sujeta al secreto profesional,
>
> cuya divulgación no está permitida por la ley. En caso de haber
>
> recibido este mensaje por error, le rogamos que, de forma inmediata,
>
> nos lo comunique mediante correo electrónico remitido a nuestra
>
> atención o a través del teléfono (+34 914531200) y proceda a su
>
> eliminación, así como a la de cualquier documento adjunto al mismo.
>
> Asimismo, le comunicamos que la distribución, copia o utilización de
>
> este mensaje, o de cualquier documento adjunto al mismo, cualquiera
>
> que fuera su finalidad, están prohibidas por la ley. Le informamos,
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> comunicaciones por medio de Internet no permiten asegurar ni
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>
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>
> asume responsabilidad alguna por tales circunstancias. Si no
>
> consintiese la utilización del correo electrónico o de las
>
> comunicaciones vía Internet le rogamos nos lo comunique y ponga en
>
> nuestro conocimiento de manera inmediata.
>
>
>
> *************** LEGAL NOTICE **************
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> This message is intended exclusively for the person to whom it is
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> addressed and contains privileged and confidential information
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> protected from disclosure by law. If you are not the addressee
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