lumi and/or beadarray for getting beadSummary
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Dick Beyer ★ 1.4k
@dick-beyer-26
Last seen 6.9 years ago
I'm hoping someone can point me in the right direction. Some months ago I analyzed some Illumina mouse data using the lumi() package since the data received was a beadSummary data file. As I sort of understand things, this is a summary file output by Illumina's GenomicStudio software (or maybe it is BeadStudio?). I now have received some more Illumina mouse data (tif, xml, loc, txt, csv, idat files), but this time it is bead data. I've used the beadarray() package to look at this data and that works just fine. What I was wondering is whether the beadarray() package can create something similar to the beadSummary data? I've read through the beadarray vignette but can't seem to figure out how to do this (or whether it is possible). Thanks very much for any help, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/members_fc_IEHSFC.html http://staff.washington.edu/dbeyer ********************************************************************** ********* On Mon, 5 Sep 2011, bioconductor-request at r-project.org wrote: > Send Bioconductor mailing list submissions to > bioconductor at r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/bioconductor > or, via email, send a message with subject or body 'help' to > bioconductor-request at r-project.org > > You can reach the person managing the list at > bioconductor-owner at r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bioconductor digest..." > > > Today's Topics: > > 1. Re: EBImage crop failure (Michael Cole) > 2. Agilent G4131F annotatin package (Jing Huang) > 3. Re: Agilent G4131F annotatin package (MacDonald, James) > 4. Re: Agilent G4131F annotatin package (Jing Huang) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 2 Sep 2011 12:22:10 -0400 > From: Michael Cole <m.cole at="" rutgers.edu=""> > To: Gregoire Pau <gregoire.pau at="" embl.de=""> > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] EBImage crop failure > Message-ID: > <camvswwtbno3kuoctzocrq=e_gjjfovm=nj+itjhd9vecbmr=qw at="" mail.gmail.com=""> > Content-Type: text/plain; charset="ISO-8859-1" > > Thanks Gregoire, > > The images are color. Can I assume img[1:200, 1:200,x] gives a cropped > image in red,blue,green where x={1,2,3}? > > Michael > > > On Fri, Sep 2, 2011 at 3:10 AM, Gregoire Pau <gregoire.pau at="" embl.de=""> wrote: >> Hello Michael, >> >> EBImage represents images as multidimensional arrays. Color images are >> usually represented as 3-dimensional ones, where the third dimension >> contains the color components. >> >> From your example, it seems that are you are manipulating 3-dimensional >> arrays, explaining why "a[1:120,50:120]" fails. Use "a[1:120,50:120,]" >> instead to crop images. >> >> Is the image you are working with is a grayscale one ? In this case, you >> are maybe manipulating an image that was stored as a color one, >> explaining your array has 3 dimensions. Doing "a = Image(a[,,1], >> color=Grayscale)" will fix this. >> >> Hope this helps, >> Cheers, >> >> Greg >> --- >> Gregoire Pau >> EMBL Research officer >> http://www.embl.de/~gpau/ >> >> On 28/08/2011 15:22, Michael Cole wrote: >>> Using the latest version of EBImage and ver 8:6.6.9.7-5 of ImageMagick (debian >>> package) several EBImage operations fail. >>> >>> In particular, cropping an image with: >>> a<-readImage("xxxxxxxx") >>> a[1:120,50:120] # fails with "incorrect number of dimensions"] >>> >>> I can get cropped images by doing: >>> a[1:120,50:120,1] # display gives correct region with a red mask >>> a[1:120,50:120,c(1,0,0)] # display gives correct region with a red mask >>> a[1:120,50:120,c(1,0,1)] # display gives correct region with a yellow mask >>> a[1:120,50:120,c(1,1,1)] # display gives correct region as grayscale >>> a[1:120,50:120,c(0,1,1)] # display gives correct region with a yellow mask >>> >>> and so on. >>> >>> Has there been a change in EBImage that is not reflected in the documentation? >>> >>> I am trying to build histograms for each color channel to build classification >>> models. >>> >>> >>> Thanks, >>> >>> Michael >>> >>> _______________________________________________ >>> 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 >> > > > > -- > Michael Cole > m.cole at rutgers.edu > > > > ------------------------------ > > Message: 2 > Date: Sun, 4 Sep 2011 12:04:44 -0700 > From: Jing Huang <huangji at="" ohsu.edu=""> > To: "'bioconductor at r-project.org'" <bioconductor at="" r-project.org=""> > Subject: [BioC] Agilent G4131F annotatin package > Message-ID: > <ea06f3966341664f9dcb57668a8587ff037c83e4a3 at="" ex-="" mb06.ohsu.edu=""> > Content-Type: text/plain > > Dear All members, > > Can somebody provide me an advice on R annotation package for GPL4135 Agilent-014879 Whole Rat Genome Microarray 4x44K G4131F (Feature Number version)? > > Many Many Thanks > > Jing Huang PhD > > OHSU, Oregon > > [[alternative HTML version deleted]] > > > ------------------------------ > > Message: 3 > Date: Sun, 4 Sep 2011 16:15:17 -0400 > From: "MacDonald, James" <jmacdon at="" med.umich.edu=""> > To: Jing Huang <huangji at="" ohsu.edu=""> > Cc: "'bioconductor at r-project.org'" <bioconductor at="" r-project.org=""> > Subject: Re: [BioC] Agilent G4131F annotatin package > Message-ID: <4E63DC55.1070105 at med.umich.edu> > Content-Type: text/plain; charset="iso-8859-1"; format="flowed" > > Hi Jing, > > On 9/4/11 3:04 PM, Jing Huang wrote: >> Dear All members, >> >> Can somebody provide me an advice on R annotation package for GPL4135 Agilent-014879 Whole Rat Genome Microarray 4x44K G4131F (Feature Number version)? > > You will have to build your own package. Please see the SQLForge vignette: > > http://www.bioconductor.org/packages/2.8/bioc/vignettes/AnnotationDb i/inst/doc/SQLForge.pdf > > Best, > > Jim > >> Many Many Thanks >> >> Jing Huang PhD >> >> OHSU, Oregon >> >> [[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 > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues > > > > ------------------------------ > > Message: 4 > Date: Sun, 4 Sep 2011 17:47:33 -0700 > From: Jing Huang <huangji at="" ohsu.edu=""> > To: "'MacDonald, James'" <jmacdon at="" med.umich.edu=""> > Cc: "'bioconductor at r-project.org'" <bioconductor at="" r-project.org=""> > Subject: Re: [BioC] Agilent G4131F annotatin package > Message-ID: > <ea06f3966341664f9dcb57668a8587ff037c83e4a4 at="" ex-="" mb06.ohsu.edu=""> > Content-Type: text/plain; charset="Windows-1252" > > THANK you Jim! > > Jing > > -----Original Message----- > From: MacDonald, James [mailto:jmacdon at med.umich.edu] > Sent: Sunday, September 04, 2011 1:15 PM > To: Jing Huang > Cc: 'bioconductor at r-project.org' > Subject: Re: [BioC] Agilent G4131F annotatin package > > Hi Jing, > > On 9/4/11 3:04 PM, Jing Huang wrote: >> Dear All members, >> >> Can somebody provide me an advice on R annotation package for GPL4135 Agilent-014879 Whole Rat Genome Microarray 4x44K G4131F (Feature Number version)? > > You will have to build your own package. Please see the SQLForge vignette: > > http://www.bioconductor.org/packages/2.8/bioc/vignettes/AnnotationDb i/inst/doc/SQLForge.pdf > > Best, > > Jim > >> Many Many Thanks >> >> Jing Huang PhD >> >> OHSU, Oregon >> >> [[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 > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues > > > > ------------------------------ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > End of Bioconductor Digest, Vol 103, Issue 4 > ******************************************** >
Microarray Annotation EBImage Microarray Annotation EBImage • 632 views
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Mike Smith ★ 5.0k
@mike-smith
Last seen 12 minutes ago
EMBL Heidelberg / de.NBI
Hi Dick, Sorry for taking a while to get back to you. Section 9 of the bead- level vignette covers how to get summary data from bead-level data: http://www.bioconductor.org/packages/2.8/bioc/vignettes/beadarray/inst /doc/beadlevel.pdf The first 4 lines from the examples code in that section will create an ExpressionSetIllumina object using the default summarisation parameters, which is what you would get if you read summary data directly into beadarray. Personally I find the need to set up the channels (the first 3 lines of the example) a bit confusing, so if you're using the developmental version of beadarray (currently version 2.3.7) we've sorted the defaults out so you can simply type: summarize(BLData) to get the summary data. I hope that's some help, -- Mike Smith PhD Student Computational Biology Group Cambridge University [[alternative HTML version deleted]]
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