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

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}}

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