Re: [aroma.affymetrix] using custom CDF file in aroma.affymetrix
I downloaded the two non-official CDFs * HTA-2_0.r1.exon.cdf * HTA-2_0.r1.gene.cdf from http://www.affymetrix.com/support/technical/byproduct.affx?product=human_transcriptome. I then renamed them to use commas instead of periods for the tags. When I inspect them I see that they report an array dimension of 2572x2680 (=6892960), whereas your CDF reports 2560x2560 (=6553600). The dimension of the CDF must much that of the CEL files. Are you sure your CDF is correct? Where did you get yours from? cdf - AffymetrixCdfFile$byChipType(HTA-2_0, tags=r1,exon) cdf AffymetrixCdfFile: Path: annotationData/chipTypes/HTA-2_0 Filename: HTA-2_0,r1,exon.cdf File size: 818.80 MB (858574387 bytes) Chip type: HTA-2_0,r1,exon RAM: 0.00MB File format: v3 (text; ASCII) Dimension: 2572x2680 Number of cells: 6892960 Number of units: 914585 Cells per unit: 7.54 Number of QC units: 0 cdf - AffymetrixCdfFile$byChipType(HTA-2_0, tags=r1,gene) cdf AffymetrixCdfFile: Path: annotationData/chipTypes/HTA-2_0 Filename: HTA-2_0,r1,gene.cdf File size: 467.96 MB (490696493 bytes) Chip type: HTA-2_0,r1,gene RAM: 0.00MB File format: v3 (text; ASCII) Dimension: 2572x2680 Number of cells: 6892960 Number of units: 70523 Cells per unit: 97.74 Number of QC units: 0 /Henrik On Thu, Oct 16, 2014 at 8:54 AM, San sood.sanj...@gmail.com wrote: Hi Henrik, Please see below: sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] preprocessCore_1.24.0 fdrtool_1.2.12 FIRMAGene_0.9.8 aroma.light_1.32.0 matrixStats_0.10.0 aroma.affymetrix_2.12.0 aroma.core_2.12.1 R.devices_2.11.0R.filesets_2.6.0 gplots_2.14.2 limma_3.18.13 class_7.3-11 [13] Biobase_2.22.0 BiocGenerics_0.8.0 R.utils_1.34.0 R.oo_1.18.0 ggplot2_1.0.0 affxparser_1.34.2 affy_1.40.0 R.methodsS3_1.6.1 loaded via a namespace (and not attached): [1] affyio_1.30.0aroma.apd_0.5.0 base64enc_0.1-2 BiocInstaller_1.12.1 bitops_1.0-6 caTools_1.17.1 colorspace_1.2-4 digest_0.6.4 DNAcopy_1.36.0 gdata_2.13.3 grid_3.0.2 gtable_0.1.2 gtools_3.4.1 KernSmooth_2.23-13 [15] MASS_7.3-35 munsell_0.4.2plyr_1.8.1 proto_0.3-10 PSCBS_0.40.4 R.cache_0.10.0 R.huge_0.8.0 R.rsp_0.19.0 Rcpp_0.11.3 reshape2_1.4 scales_0.2.4 stringr_0.6.2tools_3.0.2 zlibbioc_1.8.0 -- View this message in context: http://aroma-affymetrix.967894.n3.nabble.com/aroma-affymetrix-using-custom-CDF-file-in-aroma-affymetrix-tp4025290p4025292.html Sent from the aroma.affymetrix mailing list archive at Nabble.com. -- -- 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/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout. -- -- 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/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] using custom CDF file in aroma.affymetrix
Hi Henrik, Please see below: sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] preprocessCore_1.24.0 fdrtool_1.2.12 FIRMAGene_0.9.8 aroma.light_1.32.0 matrixStats_0.10.0 aroma.affymetrix_2.12.0 aroma.core_2.12.1 R.devices_2.11.0R.filesets_2.6.0 gplots_2.14.2 limma_3.18.13 class_7.3-11 [13] Biobase_2.22.0 BiocGenerics_0.8.0 R.utils_1.34.0 R.oo_1.18.0 ggplot2_1.0.0 affxparser_1.34.2 affy_1.40.0 R.methodsS3_1.6.1 loaded via a namespace (and not attached): [1] affyio_1.30.0aroma.apd_0.5.0 base64enc_0.1-2 BiocInstaller_1.12.1 bitops_1.0-6 caTools_1.17.1 colorspace_1.2-4 digest_0.6.4 DNAcopy_1.36.0 gdata_2.13.3 grid_3.0.2 gtable_0.1.2 gtools_3.4.1 KernSmooth_2.23-13 [15] MASS_7.3-35 munsell_0.4.2plyr_1.8.1 proto_0.3-10 PSCBS_0.40.4 R.cache_0.10.0 R.huge_0.8.0 R.rsp_0.19.0 Rcpp_0.11.3 reshape2_1.4 scales_0.2.4 stringr_0.6.2tools_3.0.2 zlibbioc_1.8.0 -- View this message in context: http://aroma-affymetrix.967894.n3.nabble.com/aroma-affymetrix-using-custom-CDF-file-in-aroma-affymetrix-tp4025290p4025292.html Sent from the aroma.affymetrix mailing list archive at Nabble.com. -- -- 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/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] using custom CDF file in aroma.affymetrix
This looks all correct to me. What is your sessionInfo() after receiving this error? /Henrik On Wed, Oct 15, 2014 at 4:19 AM, sanjana sood.sanj...@gmail.com wrote: Hi, I am using a Custom cdf file HTA-2_0,Transcript,binary.cdf in aroma. affymetrix to analyse HTA-2_0 chip . I am using the following commands to set up CDF and CEL files. chipType - HTA-2_0 cdf - AffymetrixCdfFile$byChipType(chipType, tags=Transcript,binary) print(cdf) AffymetrixCdfFile: Path: annotationData/chipTypes/HTA-2_0 Filename: HTA-2_0,Transcript,binary.cdf File size: 7.55 MB (7921066 bytes) Chip type: HTA-2_0,Transcript,binary RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2560x2560 Number of cells: 6553600 Number of units: 18490 Cells per unit: 354.44 Number of QC units: 0 cs-AffymetrixCelSet$byName(Krzy,cdf=cdf,verbose=verbose) However I am unable to read the CEL files as it gives me the following error: Error: Failed to setup a data set for any of 1 data directories located. The following reasons were reported: (1) Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'HTA-2_0' (without requiring any tags) and with filename extension 'cdf'. (while trying './rawData/Krzy/HTA-2_0'). My directory structure is: annotationData chipTypesHTA-2_0HTA-2_0,Transcript,binary.cdf rawDataKrzyHTA-2_0K15P.CEL Please can someone help me understanding what I am doing wrong. I have used aroma.affymetrix for exon arrays and I never came across this issue. Is it something to do with the CDF file? Kind Regards, Sanjana -- -- 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/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout. -- -- 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/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
