On Tue, Oct 18, 2011 at 10:59 PM, Pierre Neuvial <pie...@stat.berkeley.edu> wrote: > Hi Qian, > > I'm not sure what the warnings mean, but please see below for the error.
The warnings reporting on "In readBin(con = con, what = integer(), size = 4, n = n, signed = FALSE, : 'signed = FALSE' is only valid for integers of sizes 1 and 2" occurs with R v2.13.1 or newer and are nothing to worry about. In the next release of aroma.core that will be available (aroma.core v2.2.1 or newer) these warnings are no longer generated. /Henrik > > > On Mon, Oct 17, 2011 at 4:19 PM, Qian <littleduc...@gmail.com> wrote: >> >> Dear all, >> I just start learning aroma.affymetrix package for Affy SNP6.0 >> analysis. I downloaded ugp,ufl,acs file from the link >> http://www.aroma-project.org/chipTypes/GenomeWideSNP_6, followed the >> example code, but I got the following warnings. I can't move to the >> following steps. Would you please let me know what the problem is? >> >> Thanks a lot, >> Qian >> > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6",tags="Full"); >> > print(cdf); >> AffymetrixCdfFile: >> Path: annotationData/chipTypes/GenomeWideSNP_6 >> Filename: GenomeWideSNP_6,Full.cdf >> Filesize: 470.44MB >> Chip type: GenomeWideSNP_6,Full >> RAM: 0.00MB >> File format: v4 (binary; XDA) >> Dimension: 2572x2680 >> Number of cells: 6892960 >> Number of units: 1881415 >> Cells per unit: 3.66 >> Number of QC units: 4 >> >> > gi <- getGenomeInformation(cdf) >> Warning messages: >> 1: In readBin(con = con, what = integer(), size = 4, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 2: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 3: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 4: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 5: In readBin(con = con, what = integer(), size = 4, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 6: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 7: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 8: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> > print(gi); >> UgpGenomeInformation: >> Name: GenomeWideSNP_6 >> Tags: Full,na31,hg19,HB20110328 >> Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328 >> Pathname: annotationData/chipTypes/GenomeWideSNP_6/ >> GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp >> File size: 8.97 MB (9407867 bytes) >> RAM: 0.00 MB >> Chip type: GenomeWideSNP_6,Full >> Warning messages: >> 1: In readBin(con = con, what = integer(), size = 4, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 2: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 3: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 4: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 5: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> > si <- getSnpInformation(cdf) >> Warning messages: >> 1: In readBin(con = con, what = integer(), size = 4, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 2: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 3: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 4: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> > print(si) >> UflSnpInformation: >> Name: GenomeWideSNP_6 >> Tags: Full,na31,hg19,HB20110328 >> Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328 >> Pathname: annotationData/chipTypes/GenomeWideSNP_6/ >> GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl >> File size: 7.18 MB (7526452 bytes) >> RAM: 0.00 MB >> Chip type: GenomeWideSNP_6,Full >> Number of enzymes: 2 >> Warning messages: >> 1: In readBin(con = con, what = integer(), size = 4, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 2: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 3: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 4: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> 5: In readBin(con = con, what = integer(), size = 4, n = n, signed = >> FALSE, : >> 'signed = FALSE' is only valid for integers of sizes 1 and 2 >> > acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE)) >> > print(acs) >> AromaCellSequenceFile: >> Name: GenomeWideSNP_6 >> Tags: HB20080710 >> Full name: GenomeWideSNP_6,HB20080710 >> Pathname: annotationData/chipTypes/GenomeWideSNP_6/ >> GenomeWideSNP_6,HB20080710.acs >> File size: 170.92 MB (179217531 bytes) >> RAM: 0.00 MB >> Number of data rows: 6892960 >> File format: v1 >> Dimensions: 6892960x26 >> Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, >> raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, >> raw >> Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, >> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 >> Footer: <createdOn>20080710 22:47:02 PDT</ >> createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6</ >> chipType><srcFile><filename>GenomeWideSNP_6.probe_tab</ >> filename><filesize>341479928</ >> filesize><checksum>2037c033c09fd8f7c06bd042a77aef15</checksum></ >> srcFile><srcFile2><filename>GenomeWideSNP_6.CN_probe_tab</ >> filename><filesize>96968290</ >> filesize><checksum>3dc2d3178f5eafdbea9c8b6eca88a89c</checksum></ >> srcFile2> >> Chip type: GenomeWideSNP_6 >> Platform: Affymetrix >> There were 19 warnings (use warnings() to see them) >> > csR <- AffymetrixCelSet$byName("GenomeWideSNP_6,dataSet1", cdf=cdf) >> Error in list(`AffymetrixCelSet$byName("GenomeWideSNP_6,dataSet1", cdf >> = cdf)` = <environment>, : >> >> [2011-10-14 16:49:32] Exception: Cannot create AffymetrixCelSet. No >> such directory: GenomeWideSNP_6,dataSet1/GenomeWideSNP_6 >> at throw(Exception(...)) >> at throw.default("Cannot create ", class(static)[1], ". No such >> directory: ", path) >> at throw("Cannot create ", class(static)[1], ". No such directory: >> ", path) >> at method(static, ...) >> at AffymetrixCelSet$byName("GenomeWideSNP_6,dataSet1", cdf = cdf) > > The error message means that aroma.affymetrix could not locate your > data files. Did you follow the instructions on the page "Location of > raw data files": http://aroma-project.org/node/68 ? > > Specifically: the data files should be in > > rawData/<dataSet>/<chipType> > > where <dataSet> is the name of your data set (ie the argument you give > to "AffymetrixCelSet$byName" > and <chipType> is "GenomeWideSNP_6" in your case. > > Hope this helps, > > Pierre > >> >> > sessionInfo() >> R version 2.13.2 (2011-09-30) >> Platform: x86_64-pc-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C LC_TIME=English_United >> States.1252 >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods >> base >> >> other attached packages: >> [1] aroma.affymetrix_2.2.0 affxparser_1.24.0 >> aroma.apd_0.2.0 R.huge_0.3.0 aroma.core_2.2.0 >> aroma.light_1.21.2 >> [7] matrixStats_0.2.2 R.rsp_0.6.2 >> R.cache_0.5.2 R.filesets_1.1.0 digest_0.5.1 >> R.utils_1.8.2 >> [13] R.oo_1.8.2 R.methodsS3_1.2.1 >> >> loaded via a namespace (and not attached): >> [1] tools_2.13.2 >> >> -- >> When reporting problems on aroma.affymetrix, make sure 1) to run the latest >> version of the package, 2) to report the output of sessionInfo() and >> traceback(), and 3) to post a complete code example. >> >> >> You received this message because you are subscribed to the Google Groups >> "aroma.affymetrix" group with website http://www.aroma-project.org/. >> To post to this group, send email to aroma-affymetrix@googlegroups.com >> To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
