Search
Question: Illumina Expression analysis from iDAT files
2
gravatar for Sean Davis
4.0 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
Hi, all. I have a set of iDAT files from illumina expression arrays and have been looking around for a workflow that begins with the iDAT files. Illuminaio can read them and beadarray and lumi packages (to name a couple) can deal with illumina data normalization and processing, but I didn't find a bridge between the illuminaio output and further processing. I very well may have missed something, but I thought I would check. Thanks, Sean [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.0 years ago by Gordon Smyth32k • written 4.0 years ago by Sean Davis21k
1
gravatar for Mike Smith
4.0 years ago by
Mike Smith2.1k
EMBL Heidelberg / de.NBI
Mike Smith2.1k wrote:
Hi Sean, The short answer is that you are correct, there isn't currently a quick and easy way to read IDAT files into R and then feed the data to downstream processing packages. The inclusion of the expression IDAT reading routines in illuminaio is still fairly new compared to the support for other platforms. My hope is for downstream packages to use the reading routines from illuminaio directly, in a similar fashion to crlmm and minfi. I'm currently working on implementing this for beadarray. As a short fix you can use illuminaio to generate a text file similar to the output from GenomeStudio, but this isn't a very satisfactory solution. Let me know if you run into any difficulties, the expression reading code has not been that widely used. Cheers, Mike Smith On 26 November 2013 14:33, Sean Davis <sdavis2@mail.nih.gov> wrote: > Hi, all. > > I have a set of iDAT files from illumina expression arrays and have been > looking around for a workflow that begins with the iDAT files. Illuminaio > can read them and beadarray and lumi packages (to name a couple) can deal > with illumina data normalization and processing, but I didn't find a bridge > between the illuminaio output and further processing. I very well may have > missed something, but I thought I would check. > > Thanks, > Sean > > [[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 Research Associate Statistics & Computational Biology Laboratory Cambridge University [[alternative HTML version deleted]]
ADD COMMENTlink written 4.0 years ago by Mike Smith2.1k
Thanks, Mike, for the confirmation and for the continued work on this stuff. I wrote a quick little function that uses illuminaio readIDAT and generates a LumiBatch from the lumi package. The function doesn't have any bells-and-whistles, but it will suffice for me right now. Sean On Tue, Nov 26, 2013 at 10:07 AM, Mike Smith <grimbough@gmail.com> wrote: > Hi Sean, > > The short answer is that you are correct, there isn't currently a quick and > easy way to read IDAT files into R and then feed the data to downstream > processing packages. The inclusion of the expression IDAT reading routines > in illuminaio is still fairly new compared to the support for other > platforms. > > My hope is for downstream packages to use the reading routines from > illuminaio directly, in a similar fashion to crlmm and minfi. I'm > currently working on implementing this for beadarray. As a short fix you > can use illuminaio to generate a text file similar to the output from > GenomeStudio, but this isn't a very satisfactory solution. > > Let me know if you run into any difficulties, the expression reading code > has not been that widely used. > > Cheers, > Mike Smith > > > On 26 November 2013 14:33, Sean Davis <sdavis2@mail.nih.gov> wrote: > > > Hi, all. > > > > I have a set of iDAT files from illumina expression arrays and have been > > looking around for a workflow that begins with the iDAT files. > Illuminaio > > can read them and beadarray and lumi packages (to name a couple) can deal > > with illumina data normalization and processing, but I didn't find a > bridge > > between the illuminaio output and further processing. I very well may > have > > missed something, but I thought I would check. > > > > Thanks, > > Sean > > > > [[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 > Research Associate > Statistics & Computational Biology Laboratory > Cambridge University > > [[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 > [[alternative HTML version deleted]]
ADD REPLYlink written 4.0 years ago by Sean Davis21k
0
gravatar for Gordon Smyth
4.0 years ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:
Dear Sean and Mike, We (actually Matt Ritchie) have written a nice little function that uses readIDAT() to read the IDAT files and assembles the pieces into a data object ready for limma analysis. The output is an EList object, but it could be an ExpressionSet instead. It has been suggested that this function could be added to the limma package, but I wondered whether the illuminaio package would be the best home. What would you like us to do? Best wishes Gordon > Date: Tue, 26 Nov 2013 09:33:17 -0500 > From: Sean Davis <sdavis2 at="" mail.nih.gov=""> > To: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Subject: [BioC] Illumina Expression analysis from iDAT files > > Hi, all. > > I have a set of iDAT files from illumina expression arrays and have been > looking around for a workflow that begins with the iDAT files. Illuminaio > can read them and beadarray and lumi packages (to name a couple) can deal > with illumina data normalization and processing, but I didn't find a bridge > between the illuminaio output and further processing. I very well may have > missed something, but I thought I would check. > > Thanks, > Sean ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD COMMENTlink written 4.0 years ago by Gordon Smyth32k
Hi Gordon, Matt has kindly already sent me a copy of his script for creating the EList object. Combined with Sean's code for generating a LumiBatch and the script I'm putting together for beadarray I think we have most of the downstream expression analysis packages covered. My initial hope was that individual packages would import illuminaio (I like the elegance of having a single function in the library) and modify their data input routines to take both the text and IDAT formats. I'll discuss it with Kasper as illuminaio is ultimately his package. Cheers, Mike On 28 November 2013 02:20, Gordon K Smyth <smyth@wehi.edu.au> wrote: > Dear Sean and Mike, > > We (actually Matt Ritchie) have written a nice little function that uses > readIDAT() to read the IDAT files and assembles the pieces into a data > object ready for limma analysis. The output is an EList object, but it > could be an ExpressionSet instead. > > It has been suggested that this function could be added to the limma > package, but I wondered whether the illuminaio package would be the best > home. > > What would you like us to do? > > Best wishes > Gordon > > Date: Tue, 26 Nov 2013 09:33:17 -0500 >> From: Sean Davis <sdavis2@mail.nih.gov> >> To: "bioconductor@r-project.org" <bioconductor@r-project.org> >> Subject: [BioC] Illumina Expression analysis from iDAT files >> >> Hi, all. >> >> I have a set of iDAT files from illumina expression arrays and have been >> looking around for a workflow that begins with the iDAT files. Illuminaio >> can read them and beadarray and lumi packages (to name a couple) can deal >> with illumina data normalization and processing, but I didn't find a >> bridge >> between the illuminaio output and further processing. I very well may >> have >> missed something, but I thought I would check. >> >> Thanks, >> Sean >> > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:18}}
ADD REPLYlink written 4.0 years ago by Mike Smith2.1k
I agree here that having packages maintain their own routines probably makes sense. What I am not clear on yet is if we have all the annotation to account for the various control probes. Does anyone know? Sean Hi Gordon, Matt has kindly already sent me a copy of his script for creating the EList object. Combined with Sean's code for generating a LumiBatch and the script I'm putting together for beadarray I think we have most of the downstream expression analysis packages covered. My initial hope was that individual packages would import illuminaio (I like the elegance of having a single function in the library) and modify their data input routines to take both the text and IDAT formats. I'll discuss it with Kasper as illuminaio is ultimately his package. Cheers, Mike On 28 November 2013 02:20, Gordon K Smyth <smyth@wehi.edu.au> wrote: > Dear Sean and Mike, > > We (actually Matt Ritchie) have written a nice little function that uses > readIDAT() to read the IDAT files and assembles the pieces into a data > object ready for limma analysis. The output is an EList object, but it > could be an ExpressionSet instead. > > It has been suggested that this function could be added to the limma > package, but I wondered whether the illuminaio package would be the best > home. > > What would you like us to do? > > Best wishes > Gordon > > Date: Tue, 26 Nov 2013 09:33:17 -0500 >> From: Sean Davis <sdavis2@mail.nih.gov> >> To: "bioconductor@r-project.org" <bioconductor@r-project.org> >> Subject: [BioC] Illumina Expression analysis from iDAT files >> >> Hi, all. >> >> I have a set of iDAT files from illumina expression arrays and have been >> looking around for a workflow that begins with the iDAT files. Illuminaio >> can read them and beadarray and lumi packages (to name a couple) can deal >> with illumina data normalization and processing, but I didn't find a >> bridge >> between the illuminaio output and further processing. I very well may >> have >> missed something, but I thought I would check. >> >> Thanks, >> Sean >> > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:12}}
ADD REPLYlink written 4.0 years ago by Sean Davis21k
If you're using Mark Dunning's package, you should... library(illuminaHumanv4.db) conn <- illuminaHumanv4_dbconn() sql <- 'SELECT ReporterGroupName, COUNT(ArrayAddress) AS probes FROM ExtraInfo GROUP BY ReporterGroupName' dbGetQuery(conn, sql) ## data frame with 100 rows and 2 columns ## ReporterGroupName probes ## <character> <integer> ## 1 NA 47224 ## 2 ERCC-00002 1 ## 3 ERCC-00003 1 ## 4 ERCC-00004 1 ## 5 ERCC-00009 1 ## ... ... ... ## 96 cy3_hyb,low_stringency_hyb 4 ## 97 housekeeping 7 ## 98 labeling 2 ## 99 low_stringency_hyb 4 ## 100 negative 770 Whether the resulting mapped probes get put into the right place in a given data structure is another matter... *He that would live in peace and at ease, * *Must not speak all he knows, nor judge all he sees.* Benjamin Franklin, Poor Richard's Almanack<http: archive.org="" details="" poorrichardsalma00franrich=""> On Thu, Nov 28, 2013 at 1:53 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > I agree here that having packages maintain their own routines probably > makes sense. What I am not clear on yet is if we have all the annotation > to account for the various control probes. Does anyone know? > > Sean > Hi Gordon, > > Matt has kindly already sent me a copy of his script for creating the EList > object. Combined with Sean's code for generating a LumiBatch and the > script I'm putting together for beadarray I think we have most of the > downstream expression analysis packages covered. My initial hope was that > individual packages would import illuminaio (I like the elegance of having > a single function in the library) and modify their data input routines to > take both the text and IDAT formats. I'll discuss it with Kasper as > illuminaio is ultimately his package. > > Cheers, > > Mike > > > On 28 November 2013 02:20, Gordon K Smyth <smyth@wehi.edu.au> wrote: > > > Dear Sean and Mike, > > > > We (actually Matt Ritchie) have written a nice little function that uses > > readIDAT() to read the IDAT files and assembles the pieces into a data > > object ready for limma analysis. The output is an EList object, but it > > could be an ExpressionSet instead. > > > > It has been suggested that this function could be added to the limma > > package, but I wondered whether the illuminaio package would be the best > > home. > > > > What would you like us to do? > > > > Best wishes > > Gordon > > > > Date: Tue, 26 Nov 2013 09:33:17 -0500 > >> From: Sean Davis <sdavis2@mail.nih.gov> > >> To: "bioconductor@r-project.org" <bioconductor@r-project.org> > >> Subject: [BioC] Illumina Expression analysis from iDAT files > >> > >> Hi, all. > >> > >> I have a set of iDAT files from illumina expression arrays and have been > >> looking around for a workflow that begins with the iDAT files. > Illuminaio > >> can read them and beadarray and lumi packages (to name a couple) can > deal > >> with illumina data normalization and processing, but I didn't find a > >> bridge > >> between the illuminaio output and further processing. I very well may > >> have > >> missed something, but I thought I would check. > >> > >> Thanks, > >> Sean > >> > > > > ______________________________________________________________________ > > The information in this email is confidential and inte...{{dropped:12}} > > _______________________________________________ > 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]]
ADD REPLYlink written 4.0 years ago by Tim Triche4.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 346 users visited in the last hour