Hi Qian, I'm not sure what the warnings mean, but please see below for the error.
On Mon, Oct 17, 2011 at 4:19 PM, Qian <[email protected]> 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 [email protected] > 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 [email protected] To unsubscribe and other options, go to http://www.aroma-project.org/forum/
