it's been fixed... wait for the next build cycle and get oligo 1.16.2. b 2011/9/23 Benilton Carvalho <beniltoncarvalho at="" gmail.com="">: > thansk for the report... will address the issue and get back to the > list once it's been fixed. > > b > > 2011/9/23 Valerie Obenchain <vobencha at="" fhcrc.org="">: >> Hi Lin, >> >> Thank you for sending the files. I was able to reproduce your error. I'm >> copying the package maintainer because I think you've identified a bug >> in oligo. >> >> Benilton, there is a problem in computePSDABG() when using ff files. I >> believe the result of computeDABG() should be a matrix or data.frame. In >> this >> case it is a closed ff file. Using Lin's data which was attached to the >> previous post, >> >> library(oligo) >> library(ff) >> >> geneExp <- read.celfiles(filenames=c("GSM409113.CEL","GSM409114.CEL")) >> >> ## fails when method=SDABG : >>> callps <- paCalls(geneExp,method="PSDABG") >> Computing DABG calls... Error in log(paCalls(x, method = "DABG", verbose >> = FALSE)) : >> Non-numeric argument to mathematical function >> In addition: Warning message: >> In `[.ff_array`(exprs(x), tmp[["fid"]], , drop = FALSE) : >> opening ff /media/valdrive/intensities-16fcfbb5.ff >> >> ## completes (with warning) when method=DABG (default) : >>> callps <- paCalls(geneExp) >> Computing DABG calls... OK >> Warning message: >> In `[.ff_array`(exprs(x), tmp[["fid"]], , drop = FALSE) : >> opening ff /media/valdrive/intensities-16fcfbb5.ff >> >> ## The failure occurs in computePSDABG() at this line, >> paProbe <- -log(paCalls(x, method="DABG", verbose=FALSE)) >> >> ## Replicating this using Lin's data, we see the result is a closed fffile, >> >> res <- paCalls(geneExp, method="DABG", verbose=FALSE) >>> res <- paCalls(geneExp, method="DABG", verbose=FALSE) >> Warning message: >> In `[.ff_array`(exprs(x), tmp[["fid"]], , drop = FALSE) : >> opening ff /media/valdrive/intensities-16fcfbb5.ff >>> res >> ff (closed) double length=1722986 (1722986) dim=c(861493,2) dimorder=c(1,2) >> >>> -log(res) >> Error in log(res) : Non-numeric argument to mathematical function >> >> ## I'm not sure if you want to recast the data or keep it in the file but >> ## some manipulation will need to take place before we can take the log, >> >> open(res) >>> res >> ff (open) double length=1722986 (1722986) dim=c(861493,2) dimorder=c(1,2) >> GSM409113.CEL GSM409114.CEL >> 116371 0.780254777 0.487261146 >> 943979 0.003161222 0.242360379 >> 493089 0.003161222 0.242360379 >> 907039 0.056526208 0.149023638 >> 1033309 0.011470282 0.043795620 >> 653512 0.003099174 0.003099174 >> 690769 0.035106383 0.067021277 >> 997409 0.107438017 0.390495868 >> : : : >> >> >>> logres <- -log(as.matrix(res[,])) >>> head(logres) >> GSM409113.CEL GSM409114.CEL >> 116371 0.2481348 0.7189551 >> 943979 5.7567965 1.4173295 >> 493089 5.7567965 1.4173295 >> 907039 2.8730509 1.9036503 >> 1033309 4.4679958 3.1282215 >> 653512 5.7766198 5.7766198 >> >> >> Valerie >> >> >> >> >> >> On 09/20/2011 06:49 PM, marco wrote: >>> hello everyone. >>> here is my problem with code and output. >>> translation from Chinese to English was given when needed. >>> .gz of datafile were attached with this mail. >>> Thanks a lot!! >>> >>> Lin Pei >>> ### here is my code >>> library(oligo) >>> library(ff) >>> geneExp <- read.celfiles(filenames=c("GSM409113.CEL","GSM409114.CEL")) >>> esetps <- rma(geneExp,target="probeset") >>> callps <- paCalls(geneExp,method="PSDABG") >>> >>> ### here is the original output >>>> library(oligo) >>> ?????????oligoClasses >>> ?????????Biobase >>> >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material. To view, type >>> 'browseVignettes()'. To cite Bioconductor, see >>> 'citation("Biobase")' and for packages 'citation("pkgname")'. >>> >>> ================================================================== ============== >>> Welcome to oligoClasses version 1.14.0 >>> ================================================================== ============== >>> Large dataset support for 'oligo/crlmm': Disabled >>> - Load 'ff' >>> ================================================================== ============== >>> Parallel computing support for 'oligo/crlmm': Disabled >>> - Load 'ff' >>> - Load 'snow' >>> - Use options(cluster=makeCluster(...)) >>> ================================================================== ============== >>> ?????????preprocessCore >>> Loading package bit1.1-7 >>> >>> package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2) >>> >>> creators: bit bitwhich >>> >>> coercion: as.logical as.integer as.bit as.bitwhich which >>> >>> operator: ! & | xor != == >>> >>> querying: print length any all min max range sum summary >>> >>> bit access: length<- [ [<- [[ [[<- >>> >>> for more help type ?bit >>> >>> Loading package ff2.2-3 >>> - getOption("fftempdir")=="/tmp/RtmpsQZPOJ" >>> >>> - getOption("ffextension")=="ff" >>> >>> - getOption("ffdrop")==TRUE >>> >>> - getOption("fffinonexit")==TRUE >>> >>> - getOption("ffpagesize")==65536 >>> >>> - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if >>> your system stalls on large writes >>> >>> - getOption("ffbatchbytes")==16777216 -- consider a different value >>> for tuning your system >>> >>> - getOption("ffmaxbytes")==536870912 -- consider a different value for >>> tuning your system >>> >>> ================================================================== ============== >>> Welcome to oligo version 1.16.0 >>> ================================================================== ============== >>>> library(ff) >>> ?????????tools >>> ?????????bit >>> >>> ??????'bit' >>> >>> The following object(s) are masked from 'package:base': >>> >>> xor >>> >>> Attaching package ff >>> >>> ??????'ff' >>> >>> The following object(s) are masked from 'package:utils': >>> >>> write.csv, write.csv2 >>> >>> The following object(s) are masked from 'package:base': >>> >>> is.factor, is.ordered >>> >>> ================================================================== ============== >>> Large dataset support for 'oligo/crlmm': Enabled >>> - Probesets: 20,000 >>> - Samples..: 100 >>> - Path.....: /sdc1/linp/Data/GSE16558_RAW.tar_FILES >>> ================================================================== ============== >>>> geneExp <- read.celfiles(filenames=c("GSM409113.CEL","GSM409114.CEL")) >>> Loading required package: pd.hugene.1.0.st.v1 >>> Loading required package: RSQLite >>> Loading required package: DBI >>> Platform design info loaded. >>>> esetps <- rma(geneExp,target="probeset") >>> Background correcting... OK >>> Normalizing... OK >>> Summarizing... OK >>>> callps <- paCalls(geneExp,method="PSDABG") >>> Computing DABG calls... ???log(paCalls(x, method = "DABG", verbose = >>> FALSE)) : (translation:error in) >>> ???????????? ( translation:mathematical function use non-numeric argument) >>> ??: ?????(translation:warnings) >>> In `[.ff_array`(exprs(x), tmp[["fid"]], , drop = FALSE) : >>> opening ff /sdc1/linp/Data/GSE16558_RAW.tar_FILES/intensities- 609fb008.ff >>> >>> >>> 2011/9/21, Valerie Obenchain <vobencha at="" fhcrc.org="">: >>>> Hello, >>>> >>>> There isn't enough information here to help answer your question. >>>> Please provide a small reproducible example of your error and the output >>>> of sessionInfo(). >>>> >>>> Valerie >>>> >>>> >>>> >>>> On 09/20/2011 07:31 AM, marco wrote: >>>>> Hello Everyone >>>>> i used the function paCalls in package oligo to calculated >>>>> detection pvalue for human gene 1.0 ST array at probeset level but >>>>> fail with the error message: >>>>> "error in log(paCalls(x,method="DABG",verbose=FALSE)) >>>>> mathematical function used non-numeric parameter".( message was >>>>> translated from Chinese) >>>>> my data is GSE16558 on GEO. Package ff was loaded. >>>>> both read.celfiles() and rma() work fine. >>>>> i used paCalls by paCalls(geneExp,method="PSDABG") >>>>> Could you please give a hand? >>>>> Thanks a lot!! >>>>> >>>>> >>>> >>> >> >> _______________________________________________ >> 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 > > > > -- > Successful people ask better questions, and as a result, they get > better answers. (Tony Robbins) > -- Successful people ask better questions, and as a result, they get better answers. (Tony Robbins)