SimpleAffy: problem with Yeast Genome 2.0 Array
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Glynn, Earl ▴ 170
@glynn-earl-952
Last seen 7.3 years ago
I'm trying to use SimpleAffy with four Yeast Genome 2.0 Array GeneChips. When I ran my R script the first time, the needed cdf file seemed to be installed automatically: Background correcting trying URL 'http://bioconductor.org/packages/data/annotation/1.7/bin/windows/cont rib/2. 2/yeast2cdf_1.10.0.zip' Content type 'application/zip' length 832343 bytes opened URL downloaded 812Kb package 'yeast2cdf' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\efg\Local Settings\Temp\Rtmp1643\downloaded_packages updating HTML package descriptions Retrieving data from AffyBatch...done. Computing expression calls... ....done. scaling to a TGT of 100 ... Scale factor for: A_pot1-_mRNA_Yeast_2.CEL 0.060815902286448 Scale factor for: A_pot1-_totalRNA_Yeast_2.CEL 0.0588578984707041 Scale factor for: B_wt_mRNA_Yeast_2.CEL 0.0591585374701625 Scale factor for: B_wt_totalRNA_Yeast_2.CEL 0.0705377276149825 Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: yeast2cdf Now when I run the lines from my script manually, I seem to be stuck getting the "qc" command to recognize the Yeast Genome 2.0 Array: > x <- read.affy("SimpleAffy.txt",path=CELpath) > x.mas5 <- call.exprs(x, "mas5") Background correcting Retrieving data from AffyBatch...done. Computing expression calls... ....done. scaling to a TGT of 100 ... Scale factor for: A_pot1-_mRNA_Yeast_2.CEL 0.060815902286448 Scale factor for: A_pot1-_totalRNA_Yeast_2.CEL 0.0588578984707041 Scale factor for: B_wt_mRNA_Yeast_2.CEL 0.0591585374701625 Scale factor for: B_wt_totalRNA_Yeast_2.CEL 0.0705377276149825 > x.qc <- qc(x, x.mas5) Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: yeast2cdf Can anyone suggest what I should do to get around this problem? Thanks in advance for any help. efg -- Earl F. Glynn Scientific Programmer Stowers Institute for Medical Research
Yeast cdf simpleaffy Yeast cdf simpleaffy • 674 views
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Crispin Miller ★ 1.1k
@crispin-miller-264
Last seen 7.3 years ago
Hi Earl, This is because the package needs some information about each array type to work out QC parameters (e.g. 3'/5' ratios, etc.) The yeast genome 2.0 array is currently not represented in the package - I'll add it and let you know. Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Earl F. Glynn Sent: 08 November 2005 20:14 To: bioconductor at stat.math.ethz.ch Subject: [BioC] SimpleAffy: problem with Yeast Genome 2.0 Array I'm trying to use SimpleAffy with four Yeast Genome 2.0 Array GeneChips. When I ran my R script the first time, the needed cdf file seemed to be installed automatically: Background correcting trying URL 'http://bioconductor.org/packages/data/annotation/1.7/bin/windows/cont ri b/2. 2/yeast2cdf_1.10.0.zip' Content type 'application/zip' length 832343 bytes opened URL downloaded 812Kb package 'yeast2cdf' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\efg\Local Settings\Temp\Rtmp1643\downloaded_packages updating HTML package descriptions Retrieving data from AffyBatch...done. Computing expression calls... ....done. scaling to a TGT of 100 ... Scale factor for: A_pot1-_mRNA_Yeast_2.CEL 0.060815902286448 Scale factor for: A_pot1-_totalRNA_Yeast_2.CEL 0.0588578984707041 Scale factor for: B_wt_mRNA_Yeast_2.CEL 0.0591585374701625 Scale factor for: B_wt_totalRNA_Yeast_2.CEL 0.0705377276149825 Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: yeast2cdf Now when I run the lines from my script manually, I seem to be stuck getting the "qc" command to recognize the Yeast Genome 2.0 Array: > x <- read.affy("SimpleAffy.txt",path=CELpath) > x.mas5 <- call.exprs(x, "mas5") Background correcting Retrieving data from AffyBatch...done. Computing expression calls... ....done. scaling to a TGT of 100 ... Scale factor for: A_pot1-_mRNA_Yeast_2.CEL 0.060815902286448 Scale factor for: A_pot1-_totalRNA_Yeast_2.CEL 0.0588578984707041 Scale factor for: B_wt_mRNA_Yeast_2.CEL 0.0591585374701625 Scale factor for: B_wt_totalRNA_Yeast_2.CEL 0.0705377276149825 > x.qc <- qc(x, x.mas5) Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: yeast2cdf Can anyone suggest what I should do to get around this problem? Thanks in advance for any help. efg -- Earl F. Glynn Scientific Programmer Stowers Institute for Medical Research _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
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Jenny Drnevich ★ 2.2k
@jenny-drnevich-382
Last seen 7.3 years ago
Hi Crispin, I've run into similar errors with a variety of different chip types, e.g. E.coli2, "remapped" CDFs for human-mouse-rat (available at http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/gen omic_curated_CDF.asp ). Is there any way for the end user to modify this so I don't have to bug you every time I want to try out an unusual CDF? I looked at the code, and all the needed info about spike-in probes and qc.probes are stored in the .qcEnv. If I knew what format this data needed to be in, I could create it and then change the code to look for it elsewhere. Thanks, Jenny At 07:09 AM 11/10/2005, Crispin Miller wrote: >Hi Earl, >This is because the package needs some information about each array type >to work out QC parameters (e.g. 3'/5' ratios, etc.) The yeast genome 2.0 >array is currently not represented in the package - I'll add it and let >you know. > > >Crispin > > >-----Original Message----- >From: bioconductor-bounces at stat.math.ethz.ch >[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Earl F. >Glynn >Sent: 08 November 2005 20:14 >To: bioconductor at stat.math.ethz.ch >Subject: [BioC] SimpleAffy: problem with Yeast Genome 2.0 Array > >I'm trying to use SimpleAffy with four Yeast Genome 2.0 Array GeneChips. > >When I ran my R script the first time, the needed cdf file seemed to be >installed automatically: > >Background correcting >trying URL >'http://bioconductor.org/packages/data/annotation/1.7/bin/windows/con tri >b/2. >2/yeast2cdf_1.10.0.zip' >Content type 'application/zip' length 832343 bytes opened URL downloaded >812Kb > >package 'yeast2cdf' successfully unpacked and MD5 sums checked > >The downloaded packages are in > C:\Documents and Settings\efg\Local >Settings\Temp\Rtmp1643\downloaded_packages >updating HTML package descriptions >Retrieving data from AffyBatch...done. >Computing expression calls... >....done. >scaling to a TGT of 100 ... >Scale factor for: A_pot1-_mRNA_Yeast_2.CEL 0.060815902286448 Scale >factor for: A_pot1-_totalRNA_Yeast_2.CEL 0.0588578984707041 Scale factor >for: B_wt_mRNA_Yeast_2.CEL 0.0591585374701625 Scale factor for: >B_wt_totalRNA_Yeast_2.CEL 0.0705377276149825 Error in >qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip >type: yeast2cdf > > >Now when I run the lines from my script manually, I seem to be stuck >getting the "qc" command to recognize the Yeast Genome 2.0 Array: > > > x <- read.affy("SimpleAffy.txt",path=CELpath) > > x.mas5 <- call.exprs(x, "mas5") >Background correcting >Retrieving data from AffyBatch...done. >Computing expression calls... >....done. >scaling to a TGT of 100 ... >Scale factor for: A_pot1-_mRNA_Yeast_2.CEL 0.060815902286448 Scale >factor for: A_pot1-_totalRNA_Yeast_2.CEL 0.0588578984707041 Scale factor >for: B_wt_mRNA_Yeast_2.CEL 0.0591585374701625 Scale factor for: >B_wt_totalRNA_Yeast_2.CEL 0.0705377276149825 > > x.qc <- qc(x, x.mas5) >Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about >chip >type: yeast2cdf > >Can anyone suggest what I should do to get around this problem? > >Thanks in advance for any help. > >efg >-- >Earl F. Glynn >Scientific Programmer >Stowers Institute for Medical Research > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > >-------------------------------------------------------- > > >This email is confidential and intended solely for the use o...{{dropped}} > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu
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