Dear all, I tried to post my question on aroma.affymetrix google group twice, but for some reason it was not there. I have to try to post  my question on bioconductor. Sorry about that. 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<platform>Affymetrix</platform><chiptype>GenomeWideSNP_6<srcfile><filename>GenomeWideSNP_6.probe_tab<filesize>341479928<checksum>2037c033c09fd8f7c06bd042a77aef15</checksum><srcfile2><filename>GenomeWideSNP_6.CN_probe_tab<filesize>96968290<checksum>3dc2d3178f5eafdbea9c8b6eca88a89c</checksum> 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) > 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 [[alternative HTML version deleted]]