Hi, aside from Affy's commercial arrays we also use custom arrays, for which we built the cdf and probe packages in order to be able to analyze them with Bioconductor. So far the custom arrays and their packages have worked fine, e.g. using gcRMA (just.gcrma()). However, they result in an error with SimpleAffy (which works fine with Affy's commercial arrays). The error message seems to indicate that the respective cdf and probe packages aren't present ("I'm sorry I do not know about chip type: gngnf1musacdf"), but as a matter of fact they are. Issuing > library(gngnf1musacdf) before the qc() call has no effect (i.e., it itself succeeds, but doesn't help qc() succeed). Below is a pertinent transcript. R is v2.0.1 and simpleaffy is v1.3.2. Does anyone have any idea what's going on or how to track down the root cause, and possibly even how to fix the problem? -hilmar > library(simpleaffy) Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: reposTools Welcome to 'simpleaffy' Produced by The Paterson Institute for Cancer Research and funded by CANCER RESEARCH UK. http://bioinformatics.picr.man.ac.uk/simpleaffy mailto: microarray at picr.man.ac.uk Attaching package 'simpleaffy': The following object(s) are masked from package:datasets : volcano > x <- read.affy("covdesc.txt") > 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: MGGH05051305.CEL 1.29763874700679 Scale factor for: MGGH05051306.CEL 1.36310544263026 Scale factor for: MGGH05051307.CEL 2.37128019446524 Scale factor for: MGGH05051308.CEL 2.81635815428688 Scale factor for: MGGH05051309.CEL 1.22141352555512 Scale factor for: MGGH05051310.CEL 1.12787439983082 > qc <- qc(x,x.mas5) Error in qc.affy(unnormalised, ...) : I'm sorry I do not know about chip type: gngnf1musacdf > installed.packages() Package LibPath Version Priority Bundle affy "affy" "C:/PROGRA~1/R/rw2001/library" "1.5.8" NA NA base "base" "C:/PROGRA~1/R/rw2001/library" "2.0.1" "base" NA Biobase "Biobase" "C:/PROGRA~1/R/rw2001/library" "1.5.0" NA NA boot "boot" "C:/PROGRA~1/R/rw2001/library" "1.2-20" "recommended" NA class "class" "C:/PROGRA~1/R/rw2001/library" "7.2-10" "recommended" "VR" cluster "cluster" "C:/PROGRA~1/R/rw2001/library" "1.9.6" "recommended" NA datasets "datasets" "C:/PROGRA~1/R/rw2001/library" "2.0.1" "base" NA foreign "foreign" "C:/PROGRA~1/R/rw2001/library" "0.8-0" "recommended" NA gcrma "gcrma" "C:/PROGRA~1/R/rw2001/library" "1.1.3" NA NA gngnf1bacdf "gngnf1bacdf" "C:/PROGRA~1/R/rw2001/library" "1.4.8" NA NA gngnf1baprobe "gngnf1baprobe" "C:/PROGRA~1/R/rw2001/library" "0.0.1" NA NA gngnf1musacdf "gngnf1musacdf" "C:/PROGRA~1/R/rw2001/library" "1.4.8" NA NA gngnf1musaprobe "gngnf1musaprobe" "C:/PROGRA~1/R/rw2001/library" "0.0.1" NA NA graphics "graphics" "C:/PROGRA~1/R/rw2001/library" "2.0.1" "base" NA grDevices "grDevices" "C:/PROGRA~1/R/rw2001/library" "2.0.1" "base" NA grid "grid" "C:/PROGRA~1/R/rw2001/library" "2.0.1" "base" NA hgu133acdf "hgu133acdf" "C:/PROGRA~1/R/rw2001/library" "1.4.3" NA NA hgu133aprobe "hgu133aprobe" "C:/PROGRA~1/R/rw2001/library" "1.0" NA NA hgu95acdf "hgu95acdf" "C:/PROGRA~1/R/rw2001/library" "1.4.1" NA NA hgu95aprobe "hgu95aprobe" "C:/PROGRA~1/R/rw2001/library" "1.0" NA NA hgu95av2cdf "hgu95av2cdf" "C:/PROGRA~1/R/rw2001/library" "1.4.3" NA NA hgu95av2probe "hgu95av2probe" "C:/PROGRA~1/R/rw2001/library" "1.0" NA NA KernSmooth "KernSmooth" "C:/PROGRA~1/R/rw2001/library" "2.22-14" "recommended" NA lattice "lattice" "C:/PROGRA~1/R/rw2001/library" "0.10-14" "recommended" NA MASS "MASS" "C:/PROGRA~1/R/rw2001/library" "7.2-10" "recommended" "VR" matchprobes "matchprobes" "C:/PROGRA~1/R/rw2001/library" "1.0.12" NA NA methods "methods" "C:/PROGRA~1/R/rw2001/library" "2.0.1" "base" NA mgcv "mgcv" "C:/PROGRA~1/R/rw2001/library" "1.1-8" "recommended" NA mgu74av2cdf "mgu74av2cdf" "C:/PROGRA~1/R/rw2001/library" "1.4.3" NA NA mgu74av2probe "mgu74av2probe" "C:/PROGRA~1/R/rw2001/library" "1.0" NA NA nlme "nlme" "C:/PROGRA~1/R/rw2001/library" "3.1-53" "recommended" NA nnet "nnet" "C:/PROGRA~1/R/rw2001/library" "7.2-10" "recommended" "VR" rae230acdf "rae230acdf" "C:/PROGRA~1/R/rw2001/library" "1.4.3" NA NA rae230aprobe "rae230aprobe" "C:/PROGRA~1/R/rw2001/library" "1.0" NA NA reposTools "reposTools" "C:/PROGRA~1/R/rw2001/library" "1.5.3" NA NA rgu34acdf "rgu34acdf" "C:/PROGRA~1/R/rw2001/library" "1.4.3" NA NA rgu34aprobe "rgu34aprobe" "C:/PROGRA~1/R/rw2001/library" "1.0" NA NA rpart "rpart" "C:/PROGRA~1/R/rw2001/library" "3.1-20" "recommended" NA simpleaffy "simpleaffy" "C:/PROGRA~1/R/rw2001/library" "1.3.2" NA NA spatial "spatial" "C:/PROGRA~1/R/rw2001/library" "7.2-10" "recommended" "VR" splines "splines" "C:/PROGRA~1/R/rw2001/library" "2.0.1" "base" NA stats "stats" "C:/PROGRA~1/R/rw2001/library" "2.0.1" "base" NA stats4 "stats4" "C:/PROGRA~1/R/rw2001/library" "2.0.1" "base" NA survival "survival" "C:/PROGRA~1/R/rw2001/library" "2.15" "recommended" NA tcltk "tcltk" "C:/PROGRA~1/R/rw2001/library" "2.0.1" "base" NA tools "tools" "C:/PROGRA~1/R/rw2001/library" "2.0.1" "base" NA utils "utils" "C:/PROGRA~1/R/rw2001/library" "2.0.1" "base" NA Depends Suggests affy "R (>= 1.9.0), Biobase (>= 1.4.22), reposTools" "tkWidgets (>= 1.2.2), affydata" base NA NA Biobase "R (>= 1.9.0),tools" "widgetTools, tkWidgets" boot "R (>= 2.0.0), graphics, stats" "survival" class "R (>= 2.0.0), graphics, stats" "lattice, nlme, survival" cluster "R (>= 1.9), stats, graphics, utils" NA datasets NA NA foreign "R (>= 2.0.0)" NA gcrma "R (>= 1.9), affy (>= 1.4), matchprobes" "affydata" gngnf1bacdf NA NA gngnf1baprobe "R (>= 1.6), matchprobes (>= 1.0.12)" NA gngnf1musacdf NA NA gngnf1musaprobe "R (>= 1.6), matchprobes (>= 1.0.12)" NA graphics "grDevices" NA grDevices NA NA grid "grDevices" "lattice" hgu133acdf NA NA hgu133aprobe "R (>= 1.6), matchprobes" NA hgu95acdf NA NA hgu95aprobe "R (>= 1.6), matchprobes" NA hgu95av2cdf NA NA hgu95av2probe "R (>= 1.6), matchprobes" NA KernSmooth "R (>= 1.9.0)" "MASS" lattice "R (>= 2.0.0)" "grid" MASS "R (>= 2.0.0), graphics, stats" "lattice, nlme, survival" matchprobes "R (>= 1.8.0), Biobase (>= 1.4.1)" "hgu95av2cdf, hgu95av2probe, hu6800cdf, hu6800probe" methods NA NA mgcv "R (>= 1.9.0)" "nlme (>= 3.1-52), MASS (>= 7.2-2)" mgu74av2cdf NA NA mgu74av2probe "R (>= 1.6), matchprobes" NA nlme "graphics, stats, R(>= 2.0.0)" NA nnet "R (>= 2.0.0), graphics, stats" "lattice, nlme, survival" rae230acdf NA NA rae230aprobe "R (>= 1.6), matchprobes (>= 1.0.8)" NA reposTools "R (>= 1.8.0), tools" "XML" rgu34acdf NA NA rgu34aprobe "R (>= 1.6), matchprobes" NA rpart "R (>= 2.0.0)" "survival" simpleaffy "R (>= 1.9.0), affy" NA spatial "R (>= 2.0.0), graphics, stats" "lattice, nlme, survival" splines NA NA stats NA NA stats4 "graphics, stats, methods" NA survival "stats, utils, graphics, splines, R (>= 2.0.0)" NA tcltk NA NA tools NA NA utils NA NA > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757

Hi, Simpleaffy needs various parameters to calculate the qc values properly - these include the names of the probesets used to calculate 3'/5' ratios and so on etc. These data are stored in the package, so aren't available for your custom array. The error message you're getting is because the package can't find them ... I'll send another (longer) post later when I've worked out the best way for you to get these data in... :-) Cheers, Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Hilmar Lapp Sent: 21 June 2005 01:11 To: Bioconductor Cc: John Walker Subject: [BioC] simpleAffy, custom chip error Hi, aside from Affy's commercial arrays we also use custom arrays, for which we built the cdf and probe packages in order to be able to analyze them with Bioconductor. So far the custom arrays and their packages have worked fine, e.g. using gcRMA (just.gcrma()). However, they result in an error with SimpleAffy (which works fine with Affy's commercial arrays). The error message seems to indicate that the respective cdf and probe packages aren't present ("I'm sorry I do not know about chip type: gngnf1musacdf"), but as a matter of fact they are. Issuing > library(gngnf1musacdf) before the qc() call has no effect (i.e., it itself succeeds, but doesn't help qc() succeed). Below is a pertinent transcript. R is v2.0.1 and simpleaffy is v1.3.2. Does anyone have any idea what's going on or how to track down the root cause, and possibly even how to fix the problem? -hilmar <*SNIP*> -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}