Read .idat Illumina files in R

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Ekta Jain ▴ 370

@ekta-jain-5131

Last seen 10.2 years ago

Dear Bioc and R List Users, I am having trouble analysing illumine data generated from BeadScan. I have .idat files and JPEG images. I realise that i need bead-level summary data to be able to begin quality control followed by normalization. Is there a way i can read .idat files for expression analysis or do i need to go back to BeadScan and generate .txt files/tiff files ? Appreciate any help here. Many Thanks, Ekta Jain The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com [[alternative HTML version deleted]]

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ADD COMMENT • link updated 12.6 years ago by Moiz Bootwalla ▴ 50 • written 12.6 years ago by Ekta Jain ▴ 370

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Moiz Bootwalla ▴ 50

@moiz-bootwalla-5215

Last seen 9.7 years ago

United States

Hi Ekta, You can use the bioconductor package methylumi to read in .idat files. The function methylumIDAT() will read in .idat files and provide you with beta values along with the M and U values as a MethyLumiSet object. You can then use the functions methylumi.bgcorr() and normalizeMethyLumiSet() to background correct and normalize your data. See the vignette for more details. Best, Moiz On Apr 11, 2012, at 1:46 AM, Ekta Jain wrote: > Dear Bioc and R List Users, > I am having trouble analysing illumine data generated from BeadScan. I have .idat files and JPEG images. I realise that i need bead-level summary data to be able to begin quality control followed by normalization. Is there a way i can read .idat files for expression analysis or do i need to go back to BeadScan and generate .txt files/tiff files ? > > Appreciate any help here. > > Many Thanks, > Ekta Jain > The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, a! > nd is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. > www.jubl.com > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD COMMENT • link 12.6 years ago Moiz Bootwalla ▴ 50

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Unfortunately, this won't help for expression arrays. Last time I checked, those IDATs appeared to be encrypted. crlmm, methylumi, and minfi can all read IDAT files... *if* they are "version 3" or later (e.g. genotyping, methylation, etc). Otherwise you are probably stuck with GenomeStudio if it is expression data you're dealing with. On Wed, Apr 11, 2012 at 7:14 AM, Moiz Bootwalla <msbootwalla@gmail.com>wrote: > Hi Ekta, > > You can use the bioconductor package methylumi to read in .idat files. The > function methylumIDAT() will read in .idat files and provide you with beta > values along with the M and U values as a MethyLumiSet object. You can then > use the functions methylumi.bgcorr() and normalizeMethyLumiSet() to > background correct and normalize your data. See the vignette for more > details. > > Best, > Moiz > > > On Apr 11, 2012, at 1:46 AM, Ekta Jain wrote: > > > Dear Bioc and R List Users, > > I am having trouble analysing illumine data generated from BeadScan. I > have .idat files and JPEG images. I realise that i need bead-level summary > data to be able to begin quality control followed by normalization. Is > there a way i can read .idat files for expression analysis or do i need to > go back to BeadScan and generate .txt files/tiff files ? > > > > Appreciate any help here. > > > > Many Thanks, > > Ekta Jain > > The information contained in this electronic message and in any > attachments to this message is confidential, legally privileged and > intended only for use by the person or entity to which this electronic > message is addressed. If you are not the intended recipient, and have > received this message in error, please notify the sender and system manager > by return email and delete the message and its attachments and also you are > hereby notified that any distribution, copying, review, retransmission, > dissemination or other use of this electronic transmission or the > information contained in it is strictly prohibited. Please note that any > views or opinions presented in this email are solely those of the author > and may not represent those of the Company or bind the Company. Any > commitments made over e-mail are not financially binding on the company > unless accompanied or followed by a valid purchase order. This message has > been scanned for viruses and dangerous content by Mail Scanner,! > a! > > nd is believed to be clean. The Company accepts no liability for any > damage caused by any virus transmitted by this email. > > www.jubl.com > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]

ADD REPLY • link 12.6 years ago Tim Triche ★ 4.2k

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The expression array idats are indeed encrypted. However you can read them using the package available here: http://www.compbio.group.cam.ac.uk/Resources/IDATreader/ You can get back a data.frame containing the summarized intensity values for all bead types, along with values such as the number of beads of each type, the standard deviation with and without outliers etc. Note that this isn't the same as bead-level data. If that wasn't generated at the time of the scan there's nothing that you can do to get it from the idats and jpegs. Mike On 11 April 2012 17:49, Tim Triche, Jr. <tim.triche@gmail.com> wrote: > Unfortunately, this won't help for expression arrays. Last time I checked, > those IDATs appeared to be encrypted. > > crlmm, methylumi, and minfi can all read IDAT files... *if* they are > "version 3" or later (e.g. genotyping, methylation, etc). > > Otherwise you are probably stuck with GenomeStudio if it is expression data > you're dealing with. > > On Wed, Apr 11, 2012 at 7:14 AM, Moiz Bootwalla <msbootwalla@gmail.com> >wrote: > > > Hi Ekta, > > > > You can use the bioconductor package methylumi to read in .idat files. > The > > function methylumIDAT() will read in .idat files and provide you with > beta > > values along with the M and U values as a MethyLumiSet object. You can > then > > use the functions methylumi.bgcorr() and normalizeMethyLumiSet() to > > background correct and normalize your data. See the vignette for more > > details. > > > > Best, > > Moiz > > > > > > On Apr 11, 2012, at 1:46 AM, Ekta Jain wrote: > > > > > Dear Bioc and R List Users, > > > I am having trouble analysing illumine data generated from BeadScan. I > > have .idat files and JPEG images. I realise that i need bead-level > summary > > data to be able to begin quality control followed by normalization. Is > > there a way i can read .idat files for expression analysis or do i need > to > > go back to BeadScan and generate .txt files/tiff files ? > > > > > > Appreciate any help here. > > > > > > Many Thanks, > > > Ekta Jain > > > The information contained in this electronic message and in any > > attachments to this message is confidential, legally privileged and > > intended only for use by the person or entity to which this electronic > > message is addressed. If you are not the intended recipient, and have > > received this message in error, please notify the sender and system > manager > > by return email and delete the message and its attachments and also you > are > > hereby notified that any distribution, copying, review, retransmission, > > dissemination or other use of this electronic transmission or the > > information contained in it is strictly prohibited. Please note that any > > views or opinions presented in this email are solely those of the author > > and may not represent those of the Company or bind the Company. Any > > commitments made over e-mail are not financially binding on the company > > unless accompanied or followed by a valid purchase order. This message > has > > been scanned for viruses and dangerous content by Mail Scanner,! > > a! > > > nd is believed to be clean. The Company accepts no liability for any > > damage caused by any virus transmitted by this email. > > > www.jubl.com > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@r-project.org > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > *A model is a lie that helps you see the truth.* > * > * > Howard Skipper< > http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Mike Smith PhD Student Computational Biology Group Cambridge University [[alternative HTML version deleted]]

ADD REPLY • link 12.6 years ago Mike Smith ★ 6.6k

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