[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 21:38:52 CEST 2010
To clarify, what you suggested worked perfectly!
On Jun 30, 2010, at 3:36 PM, Richard Friedman wrote:
> 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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>> ________________________________
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>> *************** LEGAL NOTICE **************
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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
>> 914531200). In such case, you are hereby notified that any
>> dissemination, distribution, copying or use of this message or any
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>> assume any liability for those circumstances. Should you not agree
>> to the use of e-mail or to communications via Internet, you are
>> 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,
>>
>> 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 914531200). In such case, you are hereby notified that any
>>
>> dissemination, distribution, copying or use of this message or any
>>
>> attachments, for any purpose, is strictly prohibited by law. We
>>
>> hereby inform you, as addressee of this message, that e-mail and
>>
>> Internet do not guarantee the confidentiality, nor the completeness
>>
>> or proper reception of the messages sent and, thus, CNIC does not
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>> assume any liability for those circumstances. Should you not agree
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>> to the use of e-mail or to communications via Internet, you are
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>> [[alternative HTML version deleted]]
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