Illumina array analysis
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Chintanu ▴ 310
@chintanu-2646
Last seen 7.1 years ago
Hi, I'm new to my exploration with analysing illumina microarray data using r. While looking for some example case study (so that I can do my analysis taking pointers from that/those examples), I am unable to find anything useful. I would appreciate if you could either provide me with some pointers in that direction or share your codes that you have done while doing your illumina analysis. I am mainly interested in the following: (i) read in the illumina files & check the quality of the files, (iii) normalization (any type), (iii) applying Limma and pick the differentially expressed genes. Thank you. regards, Chintanu [[alternative HTML version deleted]]
Microarray Normalization limma Microarray Normalization limma • 1.2k views
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Wei Shi ★ 3.3k
@wei-shi-2183
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Australia/Melbourne/Olivia Newton-John …
Hi Chintanu, There is a case study for analyzing Illumina BeadChip data in limma user's guide. Type the following command in your R to bring up limma user's guide and then have a look at section 11.7. limmaUsersGuide() Cheers, Wei On Oct 18, 2011, at 12:55 PM, Chintanu wrote: > Hi, > > I'm new to my exploration with analysing illumina microarray data using r. > While looking for some example case study (so that I can do my analysis > taking pointers from that/those examples), I am unable to find anything > useful. I would appreciate if you could either provide me with some pointers > in that direction or share your codes that you have done while doing your > illumina analysis. > > I am mainly interested in the following: (i) read in the illumina files & > check the quality of the files, (iii) normalization (any type), (iii) > applying Limma and pick the differentially expressed genes. > > Thank you. > > regards, > Chintanu > > [[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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}
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Consider using the lumi package for normalization and data QC. Lumi implements the variance stabilization and robust spline normalization procedure that takes advantage of the multiple bead data produced by Illumina arrays. -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Wei Shi Sent: Monday, October 17, 2011 9:11 PM To: Chintanu Cc: bioc Subject: Re: [BioC] Illumina array analysis Hi Chintanu, There is a case study for analyzing Illumina BeadChip data in limma user's guide. Type the following command in your R to bring up limma user's guide and then have a look at section 11.7. limmaUsersGuide() Cheers, Wei On Oct 18, 2011, at 12:55 PM, Chintanu wrote: > Hi, > > I'm new to my exploration with analysing illumina microarray data using r. > While looking for some example case study (so that I can do my analysis > taking pointers from that/those examples), I am unable to find anything > useful. I would appreciate if you could either provide me with some pointers > in that direction or share your codes that you have done while doing your > illumina analysis. > > I am mainly interested in the following: (i) read in the illumina files & > check the quality of the files, (iii) normalization (any type), (iii) > applying Limma and pick the differentially expressed genes. > > Thank you. > > regards, > Chintanu > > [[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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:9}}
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The neqc() function in limma performs a normexp background correction (aided by control probes) and quantile normalization for the BeadChip data. For a comparison between neqc and vst used in lumi package, have a look at this paper: http://www.ncbi.nlm.nih.gov/pubmed?term=PMID%3A%2020929874 Cheers, Wei On Oct 18, 2011, at 11:33 PM, Belmont, John W wrote: > Consider using the lumi package for normalization and data QC. Lumi implements the variance stabilization and robust spline normalization procedure that takes advantage of the multiple bead data produced by Illumina arrays. > > -----Original Message----- > From: bioconductor-bounces at r-project.org [mailto:bioconductor- bounces at r-project.org] On Behalf Of Wei Shi > Sent: Monday, October 17, 2011 9:11 PM > To: Chintanu > Cc: bioc > Subject: Re: [BioC] Illumina array analysis > > Hi Chintanu, > > There is a case study for analyzing Illumina BeadChip data in limma user's guide. Type the following command in your R to bring up limma user's guide and then have a look at section 11.7. > > limmaUsersGuide() > > > Cheers, > Wei > > On Oct 18, 2011, at 12:55 PM, Chintanu wrote: > >> Hi, >> >> I'm new to my exploration with analysing illumina microarray data using r. >> While looking for some example case study (so that I can do my analysis >> taking pointers from that/those examples), I am unable to find anything >> useful. I would appreciate if you could either provide me with some pointers >> in that direction or share your codes that you have done while doing your >> illumina analysis. >> >> I am mainly interested in the following: (i) read in the illumina files & >> check the quality of the files, (iii) normalization (any type), (iii) >> applying Limma and pick the differentially expressed genes. >> >> Thank you. >> >> regards, >> Chintanu >> >> [[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 > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:18}}
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Hi, Thanks to John, Wei, and Miles Pufall. While looking at your recommended documents/vignettes, I can't seem to find any way of reading in the .idat files. In case of Affymetrix, the .cel files can be easily read in using functions like ReadAffy() from Affy package. For spotted-arrays too, the .gpr files can be read easily. I have these .idat files that I'm hoping to analyse, but am unsure regarding how I can read in the files, and (at the same time) can make use of those recommended documents/vignettes. regards, Chintanu ============================================================= > > On Oct 18, 2011, at 12:55 PM, Chintanu wrote: > > > >> Hi, > >> > >> I'm new to my exploration with analysing illumina microarray data using > r. > >> While looking for some example case study (so that I can do my analysis > >> taking pointers from that/those examples), I am unable to find anything > >> useful. I would appreciate if you could either provide me with some > pointers > >> in that direction or share your codes that you have done while doing > your > >> illumina analysis. > >> > >> I am mainly interested in the following: (i) read in the illumina files > & > >> check the quality of the files, (iii) normalization (any type), (iii) > >> applying Limma and pick the differentially expressed genes. > >> > >> Thank you. > >> > >> regards, > >> Chintanu > >> > >> [[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 > > > > > > ______________________________________________________________________ > > The information in this email is confidential and intend...{{dropped:9}} > > > > _______________________________________________ > > 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 > > > ______________________________________________________________________ > The information in this email is confidential and intended solely for the > addressee. > You must not disclose, forward, print or use it without the permission of > the sender. > ______________________________________________________________________ > [[alternative HTML version deleted]]
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Chintanu, The .idat files are only useful if you want to perform a bead-level analysis (each probe contains around ~15-30 beads). But having .idat files does not mean you have the complete bead-level data. You will have to have .txt files in your data as well, which give the intensities for each bead. But if the default setting of GenomeStudio/BeadStudio was used when your bead chips were scanned, these .txt file will NOT be outputted. This means you can not perform a bead-level analysis even you have these .idat files. In most of the microarray experiments using Illumina bead chips, only probe-level data are available. Limma starts the Illumina data analysis from reading in the probe level data (read.ilmn function), performs neqc normalization and then carry out differential expression analysis using eBayes moderated t statistics (this step is the same for all different microarray platforms). Hope this helps. Cheers, Wei On Oct 19, 2011, at 11:41 AM, Chintanu wrote: > Hi, > > Thanks to John, Wei, and Miles Pufall. > > While looking at your recommended documents/vignettes, I can't seem to find any way of reading in the .idat files. In case of Affymetrix, the .cel files can be easily read in using functions like ReadAffy() from Affy package. For spotted-arrays too, the .gpr files can be read easily. > > I have these .idat files that I'm hoping to analyse, but am unsure regarding how I can read in the files, and (at the same time) can make use of those recommended documents/vignettes. > > regards, > Chintanu > > ============================================================= > > > On Oct 18, 2011, at 12:55 PM, Chintanu wrote: > > > >> Hi, > >> > >> I'm new to my exploration with analysing illumina microarray data using r. > >> While looking for some example case study (so that I can do my analysis > >> taking pointers from that/those examples), I am unable to find anything > >> useful. I would appreciate if you could either provide me with some pointers > >> in that direction or share your codes that you have done while doing your > >> illumina analysis. > >> > >> I am mainly interested in the following: (i) read in the illumina files & > >> check the quality of the files, (iii) normalization (any type), (iii) > >> applying Limma and pick the differentially expressed genes. > >> > >> Thank you. > >> > >> regards, > >> Chintanu > >> > >> [[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 > > > > > > ______________________________________________________________________ > > The information in this email is confidential and intend...{{dropped:9}} > > > > _______________________________________________ > > 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 > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:17}}
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Hello Wei, I have inherited these .idat files, and there seems to be no way that I can get the text file(s) that you have mentioned. And, you say that I can no way make any use of these files using r, and is not a good news for me. However, I know that tools like GenePattern ( http://www.broadinstitute.org/cancer/software/genepattern/) uses .idat files; but I'm not sure whether similar to whatever process(es) being implemented at the backend of such tools can be deployed in r too !! Thank you. Cheers, Chintanu ====================================================================== == On Wed, Oct 19, 2011 at 11:55 AM, Wei Shi <shi@wehi.edu.au> wrote: > Chintanu, > > The .idat files are only useful if you want to perform a bead-level > analysis (each probe contains around ~15-30 beads). But having .idat files > does not mean you have the complete bead-level data. You will have to have > .txt files in your data as well, which give the intensities for each bead. > But if the default setting of GenomeStudio/BeadStudio was used when your > bead chips were scanned, these .txt file will NOT be outputted. This means > you can not perform a bead-level analysis even you have these .idat files. > > In most of the microarray experiments using Illumina bead chips, only > probe-level data are available. Limma starts the Illumina data analysis from > reading in the probe level data (read.ilmn function), performs neqc > normalization and then carry out differential expression analysis using > eBayes moderated t statistics (this step is the same for all different > microarray platforms). > > Hope this helps. > > Cheers, > Wei > > On Oct 19, 2011, at 11:41 AM, Chintanu wrote: > > Hi, > > Thanks to John, Wei, and Miles Pufall. > > While looking at your recommended documents/vignettes, I can't seem to find > any way of reading in the .idat files. In case of Affymetrix, the .cel files > can be easily read in using functions like ReadAffy() from Affy package. For > spotted-arrays too, the .gpr files can be read easily. > > I have these .idat files that I'm hoping to analyse, but am unsure > regarding how I can read in the files, and (at the same time) can make use > of those recommended documents/vignettes. > > regards, > Chintanu > > ============================================================= > > >> > On Oct 18, 2011, at 12:55 PM, Chintanu wrote: >> > >> >> Hi, >> >> >> >> I'm new to my exploration with analysing illumina microarray data using >> r. >> >> While looking for some example case study (so that I can do my analysis >> >> taking pointers from that/those examples), I am unable to find anything >> >> useful. I would appreciate if you could either provide me with some >> pointers >> >> in that direction or share your codes that you have done while doing >> your >> >> illumina analysis. >> >> >> >> I am mainly interested in the following: (i) read in the illumina files >> & >> >> check the quality of the files, (iii) normalization (any type), (iii) >> >> applying Limma and pick the differentially expressed genes. >> >> >> >> Thank you. >> >> >> >> regards, >> >> Chintanu >> >> >> >> [[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 >> > >> > >> > ______________________________________________________________________ >> > The information in this email is confidential and intend...{{dropped:9}} >> > >> > _______________________________________________ >> > 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 >> >> >> ______________________________________________________________________ >> The information in this email is confidential and intended solely for >> the addressee. >> You must not disclose, forward, print or use it without the permission of >> the sender. >> ______________________________________________________________________ >> > > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:10}}
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Chintanu, Would you specify the link with in Gene pattern which will use .idat files please. Thanks. Vasu From: Chintanu <chintanu@gmail.com> To: Wei Shi <shi@wehi.edu.au> Cc: bioc <bioconductor@stat.math.ethz.ch> Sent: Thursday, October 20, 2011 10:35 PM Subject: Re: [BioC] Illumina array analysis Hello Wei, I have inherited these .idat files, and there seems to be no way that I can get the text file(s) that you have mentioned. And, you say that I can no way make any use of these files using r, and is not a good news for me. However, I know that tools like GenePattern ( http://www.broadinstitute.org/cancer/software/genepattern/) uses .idat files; but I'm not sure whether similar to whatever process(es) being implemented at the backend of such tools can be deployed in r too !! Thank you. Cheers, Chintanu ====================================================================== == On Wed, Oct 19, 2011 at 11:55 AM, Wei Shi <shi@wehi.edu.au> wrote: > Chintanu, > > The .idat files are only useful if you want to perform a bead-level > analysis (each probe contains around ~15-30 beads). But having .idat files > does not mean you have the complete bead-level data. You will have to have > .txt files in your data as well,  which give the intensities for each bead. > But if the default setting of GenomeStudio/BeadStudio was used when your > bead chips were scanned, these .txt file will NOT be outputted. This means > you can not perform a bead-level analysis even you have these .idat files. > > In most of the microarray experiments using Illumina bead chips, only > probe-level data are available. Limma starts the Illumina data analysis from > reading in the probe level data (read.ilmn function), performs neqc > normalization and then carry out differential expression analysis using > eBayes moderated t statistics (this step is the same for all different > microarray platforms). > > Hope this helps. > > Cheers, > Wei > >  On Oct 19, 2011, at 11:41 AM, Chintanu wrote: > >  Hi, > > Thanks to John, Wei, and Miles Pufall. > > While looking at your recommended documents/vignettes, I can't seem to find > any way of reading in the .idat files. In case of Affymetrix, the .cel files > can be easily read in using functions like ReadAffy() from Affy package. For > spotted-arrays too, the .gpr files can be read easily. > > I have these .idat files that I'm hoping to analyse, but am unsure > regarding how I can read in the files, and (at the same time) can make use > of those recommended documents/vignettes. > > regards, > Chintanu > > ============================================================= > > >>  > On Oct 18, 2011, at 12:55 PM, Chintanu wrote: >> > >> >> Hi, >> >> >> >> I'm new to my exploration with analysing illumina microarray data using >> r. >> >> While looking for some example case study (so that I can do my analysis >> >> taking pointers from that/those examples), I am unable to find anything >> >> useful. I would appreciate if you could either provide me with some >> pointers >> >> in that direction or share your codes that you have done while doing >> your >> >> illumina analysis. >> >> >> >> I am mainly interested in the following: (i) read in the illumina files >> & >> >> check the quality of the files, (iii) normalization (any type), (iii) >> >> applying Limma and pick the differentially expressed genes. >> >> >> >> Thank you. >> >> >> >> regards, >> >> Chintanu >> >> >> >>      [[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 >> > >> > >> > ______________________________________________________________________ >> > The information in this email is confidential and intend...{{dropped:9}} >> > >> > _______________________________________________ >> > 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 >> >> >> ______________________________________________________________________ >>  The information in this email is confidential and intended solely for >> the addressee. >> You must not disclose, forward, print or use it without the permission of >> the sender. >> ______________________________________________________________________ >> > > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:11}}
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Many thanks to Wei for providing the information. Vasu: Within GenePattern ( http://genepattern.broadinstitute.org/gp/pages/login.jsf), use the module called "IlluminaExpressionFileCreator" (help file's available here: http://tinyurl.com/43n42et). This creates GCT files from a set of Illumina expression IDAT files. The .gct files can then be used for any downstream analysis. However, I am not sure how to do something similar in R to make use of the .dat files. Any comments welcome. Thank you. Cheers, Chintanu ================================================== On Fri, Oct 21, 2011 at 5:59 PM, vasu punj <punjv@yahoo.com> wrote: > Chintanu, > > Would you specify the link with in Gene pattern which will use .idat files > please. > Thanks. > > Vasu > > *From:* Chintanu <chintanu@gmail.com> > *To:* Wei Shi <shi@wehi.edu.au> > *Cc:* bioc <bioconductor@stat.math.ethz.ch> > *Sent:* Thursday, October 20, 2011 10:35 PM > > *Subject:* Re: [BioC] Illumina array analysis > > Hello Wei, > > I have inherited these .idat files, and there seems to be no way that I can > get the text file(s) that you have mentioned. And, you say that I can no > way > make any use of these files using r, and is not a good news for me. > > However, I know that tools like GenePattern ( > http://www.broadinstitute.org/cancer/software/genepattern/) uses .idat > files; but I'm not sure whether similar to whatever process(es) being > implemented at the backend of such tools can be deployed in r too !! > Thank you. > > Cheers, > Chintanu > > ==================================================================== ==== > On Wed, Oct 19, 2011 at 11:55 AM, Wei Shi <shi@wehi.edu.au> wrote: > > > Chintanu, > > > > The .idat files are only useful if you want to perform a bead- level > > analysis (each probe contains around ~15-30 beads). But having .idat > files > > does not mean you have the complete bead-level data. You will have to > have > > .txt files in your data as well, which give the intensities for each > bead. > > But if the default setting of GenomeStudio/BeadStudio was used when your > > bead chips were scanned, these .txt file will NOT be outputted. This > means > > you can not perform a bead-level analysis even you have these .idat > files. > > > > In most of the microarray experiments using Illumina bead chips, only > > probe-level data are available. Limma starts the Illumina data analysis > from > > reading in the probe level data (read.ilmn function), performs neqc > > normalization and then carry out differential expression analysis using > > eBayes moderated t statistics (this step is the same for all different > > microarray platforms). > > > > Hope this helps. > > > > Cheers, > > Wei > > > > On Oct 19, 2011, at 11:41 AM, Chintanu wrote: > > > > Hi, > > > > Thanks to John, Wei, and Miles Pufall. > > > > While looking at your recommended documents/vignettes, I can't seem to > find > > any way of reading in the .idat files. In case of Affymetrix, the .cel > files > > can be easily read in using functions like ReadAffy() from Affy package. > For > > spotted-arrays too, the .gpr files can be read easily. > > > > I have these .idat files that I'm hoping to analyse, but am unsure > > regarding how I can read in the files, and (at the same time) can make > use > > of those recommended documents/vignettes. > > > > regards, > > Chintanu > > > > ============================================================= > > > > > >> > On Oct 18, 2011, at 12:55 PM, Chintanu wrote: > >> > > >> >> Hi, > >> >> > >> >> I'm new to my exploration with analysing illumina microarray data > using > >> r. > >> >> While looking for some example case study (so that I can do my > analysis > >> >> taking pointers from that/those examples), I am unable to find > anything > >> >> useful. I would appreciate if you could either provide me with some > >> pointers > >> >> in that direction or share your codes that you have done while doing > >> your > >> >> illumina analysis. > >> >> > >> >> I am mainly interested in the following: (i) read in the illumina > files > >> & > >> >> check the quality of the files, (iii) normalization (any type), (iii) > >> >> applying Limma and pick the differentially expressed genes. > >> >> > >> >> Thank you. > >> >> > >> >> regards, > >> >> Chintanu > >> >> > >> >> [[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 > >> > > >> > > >> > ______________________________________________________________________ > >> > The information in this email is confidential and > intend...{{dropped:9}} > >> > > >> > _______________________________________________ > >> > 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 > >> > >> > >> ______________________________________________________________________ > >> The information in this email is confidential and intended solely for > >> the addressee. > >> You must not disclose, forward, print or use it without the permission > of > >> the sender. > >> ______________________________________________________________________ > >> > > > > > > > > ______________________________________________________________________ > > The information in this email is confidential and inte...{{dropped:10}} > > > _______________________________________________ > 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 > > > [[alternative HTML version deleted]]
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If memory serves, the IDAT files for Illumina expression arrays are encrypted. A student here looked into this. For genotyping and Infinium methylation arrays, it is a solved problem (Keith Baggerly wrote the original code which Matt Ritchie adapted for the crlmm package, which I in turn adapted for methylumi, and more recently Kasper Daniel Hansen renovated the code yet again within crlmm to lay groundwork for the minfi package). My understanding is that the binary files from the expression arrays are not so easy to parse. On Mon, Oct 24, 2011 at 3:48 PM, Chintanu <chintanu@gmail.com> wrote: > Many thanks to Wei for providing the information. > > Vasu: Within GenePattern ( > http://genepattern.broadinstitute.org/gp/pages/login.jsf), use the module > called "IlluminaExpressionFileCreator" (help file's available here: > http://tinyurl.com/43n42et). This creates GCT files from a set of Illumina > expression IDAT files. The .gct files can then be used for any downstream > analysis. > > However, I am not sure how to do something similar in R to make use of the > .dat files. > Any comments welcome. > > Thank you. > > Cheers, > Chintanu > > ================================================== > > On Fri, Oct 21, 2011 at 5:59 PM, vasu punj <punjv@yahoo.com> wrote: > > > Chintanu, > > > > Would you specify the link with in Gene pattern which will use .idat > files > > please. > > Thanks. > > > > Vasu > > > > *From:* Chintanu <chintanu@gmail.com> > > *To:* Wei Shi <shi@wehi.edu.au> > > *Cc:* bioc <bioconductor@stat.math.ethz.ch> > > *Sent:* Thursday, October 20, 2011 10:35 PM > > > > *Subject:* Re: [BioC] Illumina array analysis > > > > Hello Wei, > > > > I have inherited these .idat files, and there seems to be no way that I > can > > get the text file(s) that you have mentioned. And, you say that I can no > > way > > make any use of these files using r, and is not a good news for me. > > > > However, I know that tools like GenePattern ( > > http://www.broadinstitute.org/cancer/software/genepattern/) uses .idat > > files; but I'm not sure whether similar to whatever process(es) being > > implemented at the backend of such tools can be deployed in r too !! > > Thank you. > > > > Cheers, > > Chintanu > > > > ================================================================== ====== > > On Wed, Oct 19, 2011 at 11:55 AM, Wei Shi <shi@wehi.edu.au> wrote: > > > > > Chintanu, > > > > > > The .idat files are only useful if you want to perform a bead- level > > > analysis (each probe contains around ~15-30 beads). But having .idat > > files > > > does not mean you have the complete bead-level data. You will have to > > have > > > .txt files in your data as well, which give the intensities for each > > bead. > > > But if the default setting of GenomeStudio/BeadStudio was used when > your > > > bead chips were scanned, these .txt file will NOT be outputted. This > > means > > > you can not perform a bead-level analysis even you have these .idat > > files. > > > > > > In most of the microarray experiments using Illumina bead chips, only > > > probe-level data are available. Limma starts the Illumina data analysis > > from > > > reading in the probe level data (read.ilmn function), performs neqc > > > normalization and then carry out differential expression analysis using > > > eBayes moderated t statistics (this step is the same for all different > > > microarray platforms). > > > > > > Hope this helps. > > > > > > Cheers, > > > Wei > > > > > > On Oct 19, 2011, at 11:41 AM, Chintanu wrote: > > > > > > Hi, > > > > > > Thanks to John, Wei, and Miles Pufall. > > > > > > While looking at your recommended documents/vignettes, I can't seem to > > find > > > any way of reading in the .idat files. In case of Affymetrix, the .cel > > files > > > can be easily read in using functions like ReadAffy() from Affy > package. > > For > > > spotted-arrays too, the .gpr files can be read easily. > > > > > > I have these .idat files that I'm hoping to analyse, but am unsure > > > regarding how I can read in the files, and (at the same time) can make > > use > > > of those recommended documents/vignettes. > > > > > > regards, > > > Chintanu > > > > > > ============================================================= > > > > > > > > >> > On Oct 18, 2011, at 12:55 PM, Chintanu wrote: > > >> > > > >> >> Hi, > > >> >> > > >> >> I'm new to my exploration with analysing illumina microarray data > > using > > >> r. > > >> >> While looking for some example case study (so that I can do my > > analysis > > >> >> taking pointers from that/those examples), I am unable to find > > anything > > >> >> useful. I would appreciate if you could either provide me with some > > >> pointers > > >> >> in that direction or share your codes that you have done while > doing > > >> your > > >> >> illumina analysis. > > >> >> > > >> >> I am mainly interested in the following: (i) read in the illumina > > files > > >> & > > >> >> check the quality of the files, (iii) normalization (any type), > (iii) > > >> >> applying Limma and pick the differentially expressed genes. > > >> >> > > >> >> Thank you. > > >> >> > > >> >> regards, > > >> >> Chintanu > > >> >> > > >> >> [[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 > > >> > > > >> > > > >> > > ______________________________________________________________________ > > >> > The information in this email is confidential and > > intend...{{dropped:9}} > > >> > > > >> > _______________________________________________ > > >> > 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 > > >> > > >> > > >> ______________________________________________________________________ > > >> The information in this email is confidential and intended solely for > > >> the addressee. > > >> You must not disclose, forward, print or use it without the permission > > of > > >> the sender. > > >> ______________________________________________________________________ > > >> > > > > > > > > > > > > ______________________________________________________________________ > > > The information in this email is confidential and inte...{{dropped:10}} > > > > > > _______________________________________________ > > 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 > > > > > > > > [[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 > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]
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Thanks Chinatanu, � Vasu To: Chintanu <chintanu@gmail.com> Cc: vasu punj <punjv@yahoo.com>; bioc <bioconductor@stat.math.ethz.ch> Sent: Monday, October 24, 2011 4:30 PM Subject: Re: [BioC] Illumina array analysis If memory serves, the IDAT files for Illumina expression arrays are encrypted. �A student here looked into this. For genotyping and Infinium methylation arrays, it is a solved problem (Keith Baggerly wrote the original code which Matt Ritchie adapted for the crlmm package, which I in turn adapted for methylumi, and more recently Kasper Daniel Hansen renovated the code yet again within crlmm to lay groundwork for the minfi package). �My understanding is that the binary files from the expression arrays are not so easy to parse. On Mon, Oct 24, 2011 at 3:48 PM, Chintanu <chintanu@gmail.com> wrote: Many thanks to Wei for providing the information. > >Vasu: Within GenePattern ( >http://genepattern.broadinstitute.org/gp/pages/login.jsf), use the module >called "IlluminaExpressionFileCreator" (help file's available here: >http://tinyurl.com/43n42et). This creates GCT files from a set of Illumina >expression IDAT files. The .gct files can then be used for any downstream >analysis. > >However, I am not sure how to do something similar in R to make use of the >.dat files. >Any comments welcome. > >Thank you. > >Cheers, >Chintanu > >================================================== > > >On Fri, Oct 21, 2011 at 5:59 PM, vasu punj <punjv@yahoo.com> wrote: > >> �Chintanu, >> >> Would you specify the link with in Gene pattern which will use .idat files >> please. >> Thanks. >> >> Vasu >> >> �*From:* Chintanu <chintanu@gmail.com> >> *To:* Wei Shi <shi@wehi.edu.au> >> *Cc:* bioc <bioconductor@stat.math.ethz.ch> >> *Sent:* Thursday, October 20, 2011 10:35 PM >> >> *Subject:* Re: [BioC] Illumina array analysis > >> >> Hello Wei, >> >> I have inherited these .idat files, and there seems to be no way that I can >> get the text file(s) that you have mentioned. And, you say that I can no >> way >> make any use of these files using r, and is not a good news for me. >> >> However, I know that tools like GenePattern ( >> http://www.broadinstitute.org/cancer/software/genepattern/) uses .idat >> files; but I'm not sure whether similar to whatever process(es) being >> implemented at the backend of such tools can be deployed in r too !! >> Thank you. >> >> Cheers, >> Chintanu >> >> =================================================================== ===== >> On Wed, Oct 19, 2011 at 11:55 AM, Wei Shi <shi@wehi.edu.au> wrote: >> >> > Chintanu, >> > >> > The .idat files are only useful if you want to perform a bead- level >> > analysis (each probe contains around ~15-30 beads). But having .idat >> files >> > does not mean you have the complete bead-level data. You will have to >> have >> > .txt files in your data as well, �which give the intensities for each >> bead. >> > But if the default setting of GenomeStudio/BeadStudio was used when your >> > bead chips were scanned, these .txt file will NOT be outputted. This >> means >> > you can not perform a bead-level analysis even you have these .idat >> files. >> > >> > In most of the microarray experiments using Illumina bead chips, only >> > probe-level data are available. Limma starts the Illumina data analysis >> from >> > reading in the probe level data (read.ilmn function), performs neqc >> > normalization and then carry out differential expression analysis using >> > eBayes moderated t statistics (this step is the same for all different >> > microarray platforms). >> > >> > Hope this helps. >> > >> > Cheers, >> > Wei >> > >> > �On Oct 19, 2011, at 11:41 AM, Chintanu wrote: >> > >> > �Hi, >> > >> > Thanks to John, Wei, and Miles Pufall. >> > >> > While looking at your recommended documents/vignettes, I can't seem to >> find >> > any way of reading in the .idat files. In case of Affymetrix, the .cel >> files >> > can be easily read in using functions like ReadAffy() from Affy package. >> For >> > spotted-arrays too, the .gpr files can be read easily. >> > >> > I have these .idat files that I'm hoping to analyse, but am unsure >> > regarding how I can read in the files, and (at the same time) can make >> use >> > of those recommended documents/vignettes. >> > >> > regards, >> > Chintanu >> > >> > ============================================================= >> > >> > >> >> �> On Oct 18, 2011, at 12:55 PM, Chintanu wrote: >> >> > >> >> >> Hi, >> >> >> >> >> >> I'm new to my exploration with analysing illumina microarray data >> using >> >> r. >> >> >> While looking for some example case study (so that I can do my >> analysis >> >> >> taking pointers from that/those examples), I am unable to find >> anything >> >> >> useful. I would appreciate if you could either provide me with some >> >> pointers >> >> >> in that direction or share your codes that you have done while doing >> >> your >> >> >> illumina analysis. >> >> >> >> >> >> I am mainly interested in the following: (i) read in the illumina >> files >> >> & >> >> >> check the quality of the files, (iii) normalization (any type), (iii) >> >> >> applying Limma and pick the differentially expressed genes. >> >> >> >> >> >> Thank you. >> >> >> >> >> >> regards, >> >> >> Chintanu >> >> >> >> >> >> � � �[[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 >> >> > >> >> > >> >> > ______________________________________________________________________ >> >> > The information in this email is confidential and >> intend...{{dropped:9}} >> >> > >> >> > _______________________________________________ >> >> > 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 >> >> >> >> >> >> ______________________________________________________________________ >> >> �The information in this email is confidential and intended solely for >> >> the addressee. >> >> You must not disclose, forward, print or use it without the permission >> of >> >> the sender. >> >> ______________________________________________________________________ >> >> >> > >> > >> > >> > ______________________________________________________________________ >> > The information in this email is confidential and inte...{{dropped:10}} > >> >> >> _______________________________________________ >> 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 >> >> >> > >� � � �[[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 > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann [[alternative HTML version deleted]]
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Hi Chintanu, Unfortunately, there is no way you can get those text files because your bead chips have now all degraded and you can re-scan them. But why do you need to make use of these .idat files? You can still do a good analysis using the probe level data. Wei On Oct 21, 2011, at 4:35 PM, Chintanu wrote: > Hello Wei, > > I have inherited these .idat files, and there seems to be no way that I can get the text file(s) that you have mentioned. And, you say that I can no way make any use of these files using r, and is not a good news for me. > > However, I know that tools like GenePattern (http://www.broadinstitute.org/cancer/software/genepattern/) uses .idat files; but I'm not sure whether similar to whatever process(es) being implemented at the backend of such tools can be deployed in r too !! > Thank you. > > Cheers, > Chintanu > > ==================================================================== ==== > On Wed, Oct 19, 2011 at 11:55 AM, Wei Shi <shi@wehi.edu.au> wrote: > Chintanu, > > The .idat files are only useful if you want to perform a bead-level analysis (each probe contains around ~15-30 beads). But having .idat files does not mean you have the complete bead-level data. You will have to have .txt files in your data as well, which give the intensities for each bead. But if the default setting of GenomeStudio/BeadStudio was used when your bead chips were scanned, these .txt file will NOT be outputted. This means you can not perform a bead-level analysis even you have these .idat files. > > In most of the microarray experiments using Illumina bead chips, only probe-level data are available. Limma starts the Illumina data analysis from reading in the probe level data (read.ilmn function), performs neqc normalization and then carry out differential expression analysis using eBayes moderated t statistics (this step is the same for all different microarray platforms). > > Hope this helps. > > Cheers, > Wei > > On Oct 19, 2011, at 11:41 AM, Chintanu wrote: > >> Hi, >> >> Thanks to John, Wei, and Miles Pufall. >> >> While looking at your recommended documents/vignettes, I can't seem to find any way of reading in the .idat files. In case of Affymetrix, the .cel files can be easily read in using functions like ReadAffy() from Affy package. For spotted-arrays too, the .gpr files can be read easily. >> >> I have these .idat files that I'm hoping to analyse, but am unsure regarding how I can read in the files, and (at the same time) can make use of those recommended documents/vignettes. >> >> regards, >> Chintanu >> >> ============================================================= >> >> > On Oct 18, 2011, at 12:55 PM, Chintanu wrote: >> > >> >> Hi, >> >> >> >> I'm new to my exploration with analysing illumina microarray data using r. >> >> While looking for some example case study (so that I can do my analysis >> >> taking pointers from that/those examples), I am unable to find anything >> >> useful. I would appreciate if you could either provide me with some pointers >> >> in that direction or share your codes that you have done while doing your >> >> illumina analysis. >> >> >> >> I am mainly interested in the following: (i) read in the illumina files & >> >> check the quality of the files, (iii) normalization (any type), (iii) >> >> applying Limma and pick the differentially expressed genes. >> >> >> >> Thank you. >> >> >> >> regards, >> >> Chintanu >> >> >> >> [[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 >> > >> > >> > ______________________________________________________________________ >> > The information in this email is confidential and intend...{{dropped:9}} >> > >> > _______________________________________________ >> > 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 >> >> >> ______________________________________________________________________ >> The information in this email is confidential and intended solely for the addressee. >> You must not disclose, forward, print or use it without the permission of the sender. >> ______________________________________________________________________ >> > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:17}}
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Sorry, I meant to say you could not re-scan your bead chips. On Oct 21, 2011, at 4:46 PM, Wei Shi wrote: > Hi Chintanu, > > Unfortunately, there is no way you can get those text files because your bead chips have now all degraded and you can re-scan them. But why do you need to make use of these .idat files? You can still do a good analysis using the probe level data. > > Wei > > On Oct 21, 2011, at 4:35 PM, Chintanu wrote: > >> Hello Wei, >> >> I have inherited these .idat files, and there seems to be no way that I can get the text file(s) that you have mentioned. And, you say that I can no way make any use of these files using r, and is not a good news for me. >> >> However, I know that tools like GenePattern (http://www.broadinstitute.org/cancer/software/genepattern/) uses .idat files; but I'm not sure whether similar to whatever process(es) being implemented at the backend of such tools can be deployed in r too !! >> Thank you. >> >> Cheers, >> Chintanu >> >> =================================================================== ===== >> On Wed, Oct 19, 2011 at 11:55 AM, Wei Shi <shi@wehi.edu.au> wrote: >> Chintanu, >> >> The .idat files are only useful if you want to perform a bead-level analysis (each probe contains around ~15-30 beads). But having .idat files does not mean you have the complete bead-level data. You will have to have .txt files in your data as well, which give the intensities for each bead. But if the default setting of GenomeStudio/BeadStudio was used when your bead chips were scanned, these .txt file will NOT be outputted. This means you can not perform a bead-level analysis even you have these .idat files. >> >> In most of the microarray experiments using Illumina bead chips, only probe-level data are available. Limma starts the Illumina data analysis from reading in the probe level data (read.ilmn function), performs neqc normalization and then carry out differential expression analysis using eBayes moderated t statistics (this step is the same for all different microarray platforms). >> >> Hope this helps. >> >> Cheers, >> Wei >> >> On Oct 19, 2011, at 11:41 AM, Chintanu wrote: >> >>> Hi, >>> >>> Thanks to John, Wei, and Miles Pufall. >>> >>> While looking at your recommended documents/vignettes, I can't seem to find any way of reading in the .idat files. In case of Affymetrix, the .cel files can be easily read in using functions like ReadAffy() from Affy package. For spotted-arrays too, the .gpr files can be read easily. >>> >>> I have these .idat files that I'm hoping to analyse, but am unsure regarding how I can read in the files, and (at the same time) can make use of those recommended documents/vignettes. >>> >>> regards, >>> Chintanu >>> >>> ============================================================= >>> >>> > On Oct 18, 2011, at 12:55 PM, Chintanu wrote: >>> > >>> >> Hi, >>> >> >>> >> I'm new to my exploration with analysing illumina microarray data using r. >>> >> While looking for some example case study (so that I can do my analysis >>> >> taking pointers from that/those examples), I am unable to find anything >>> >> useful. I would appreciate if you could either provide me with some pointers >>> >> in that direction or share your codes that you have done while doing your >>> >> illumina analysis. >>> >> >>> >> I am mainly interested in the following: (i) read in the illumina files & >>> >> check the quality of the files, (iii) normalization (any type), (iii) >>> >> applying Limma and pick the differentially expressed genes. >>> >> >>> >> Thank you. >>> >> >>> >> regards, >>> >> Chintanu >>> >> >>> >> [[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 >>> > >>> > >>> > ______________________________________________________________________ >>> > The information in this email is confidential and intend...{{dropped:9}} >>> > >>> > _______________________________________________ >>> > 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 >>> >>> >>> ______________________________________________________________________ >>> The information in this email is confidential and intended solely for the addressee. >>> You must not disclose, forward, print or use it without the permission of the sender. >>> ______________________________________________________________________ >>> >> >> >> ______________________________________________________________________ >> The information in this email is confidential and intended solely for the addressee. >> You must not disclose, forward, print or use it without the permission of the sender. >> ______________________________________________________________________ >> > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:8}}
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