[aroma.affymetrix] Affy methylation tiling arrays - comparison of multiple groups
Hi I have multiple Affy methylation tiling arrays, (i.e. _me and _in) arrays which have been sorted into functional groups, i.e. group 1 (cancer), group 2 (cancer) and group 3 (normal) I normally run Illumina arrays for methylation and so I'm not massively confident with this platform. I've managed to import my arrays in, and analyse them with regionStats. What I want to do is try a probe level comparison of the three groups, i.e. group 1 vs. group 2; group 1 vs. group 3 and group 2 vs. group 3 for significance, i.e. I need a coefficent and p-value. I would normally use limma to construct a model, but I can't see how limma could be applied to the dataset output by regionStats Has anyone any experience with his? BW Andrew -- -- 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/groups/opt_out.
[aroma.affymetrix] Re: Affy methylation tiling arrays - comparison of multiple groups
PS Here is my sessionInfo() sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 [2] BiocInstaller_1.8.3 [3] biomaRt_2.14.0 [4] preprocessCore_1.20.0 [5] limma_3.14.4 [6] GenomicFeatures_1.10.2 [7] AnnotationDbi_1.20.5 [8] Biobase_2.18.0 [9] gsmoothr_0.1.5 [10] Repitools_1.4.0 [11] GenomicRanges_1.10.7 [12] BiocGenerics_0.4.0 [13] aroma.affymetrix_2.8.0 [14] affxparser_1.30.2 [15] aroma.apd_0.2.3 [16] R.huge_0.4.1 [17] aroma.light_1.28.0 [18] aroma.core_2.8.0 [19] matrixStats_0.6.2 [20] R.rsp_0.8.2 [21] R.devices_2.1.3 [22] R.cache_0.6.5 [23] R.filesets_2.0.0 [24] R.utils_1.19.5 [25] R.oo_1.11.7 [26] affy_1.36.1 [27] IRanges_1.16.6 [28] R.methodsS3_1.4.2 loaded via a namespace (and not attached): [1] affyio_1.26.0 Biostrings_2.26.3 bitops_1.0-5 BSgenome_1.26.1 [5] DBI_0.2-5 digest_0.6.3 edgeR_3.0.8 parallel_2.15.2 [9] PSCBS_0.30.0 RCurl_1.95-3 Rsamtools_1.10.2 RSQLite_0.11.2 [13] rtracklayer_1.18.2 stats4_2.15.2 tools_2.15.2 XML_3.95-0.1 [17] zlibbioc_1.4.0 On Monday, March 4, 2013 3:24:13 PM UTC, Andrew Beggs wrote: Hi I have multiple Affy methylation tiling arrays, (i.e. _me and _in) arrays which have been sorted into functional groups, i.e. group 1 (cancer), group 2 (cancer) and group 3 (normal) I normally run Illumina arrays for methylation and so I'm not massively confident with this platform. I've managed to import my arrays in, and analyse them with regionStats. What I want to do is try a probe level comparison of the three groups, i.e. group 1 vs. group 2; group 1 vs. group 3 and group 2 vs. group 3 for significance, i.e. I need a coefficent and p-value. I would normally use limma to construct a model, but I can't see how limma could be applied to the dataset output by regionStats Has anyone any experience with his? BW Andrew -- -- 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/groups/opt_out.
Re: [aroma.affymetrix] Re: Error in getGenomeInformation
thanks Henrik. The output is: [1] GenomeWideSNP_6,Full.cdf [2] GenomeWideSNP_6,HB20080710.acs [3] GenomeWideSNP_6,na31,hg19,HB20110328.ufl [4] GenomeWideSNP_6,na31,hg19,HB20110328.ugp On Tuesday, June 26, 2012 11:51:49 PM UTC-4, Henrik Bengtsson wrote: Following the troubleshooting of annotationData/ on http://aroma-project.org/troubleshooting/DirectoryStructures using chipType - GenomeWideSNP_6, what does print(list.files(path=path)) output? /Henrik On Tue, Jun 26, 2012 at 8:04 PM, Andrew andysure...@gmail.com wrote: I feel it might be better to post my question in this thread, as I have encountered the same error. I've downloaded ufl, ugp, and acs files from AROMA SNP6 webpage, and the Full cdf file from Affymetrix. And I still got the same kind error NT_CMU got for getGenomeInformation. Could you please give me a hint, where should I look for? Thanks! On Monday, June 18, 2012 4:58:19 PM UTC-4, NT_CMU wrote: Hi I'm trying to run the command doCRMAv2, and i get these errors. Let me know what the problem is, if any of you have encountered this before. I thought i did not have some library installed but, i have both ACNE and aroma.affymetrix working properly. ds - doCRMAv2(LeeAV_2012,chipType=GenomeWideSNP_6,Full) Error in getGenomeInformation.AffymetrixCdfFile(cdf) : [2012-06-18 16:55:10] Exception: Failed to retrieve genome information for this chip type: GenomeWideSNP_6 at #12. getGenomeInformation.AffymetrixCdfFile(cdf) - getGenomeInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #11. getGenomeInformation(cdf) - getGenomeInformation() is in environment 'aroma.affymetrix' at #10. getSubsetToAvg.AllelicCrosstalkCalibration(this) - getSubsetToAvg.AllelicCrosstalkCalibration() is in environment 'aroma.affymetrix' at #09. getSubsetToAvg(this) - getSubsetToAvg() is in environment 'aroma.affymetrix' at #08. getParameters.AllelicCrosstalkCalibration(this) - getParameters.AllelicCrosstalkCalibration() is in environment 'aroma.affymetrix' at #07. getParameters(this) - getParameters() is in environment 'R.rsp' at #06. process.AllelicCrosstalkCalibration(acc, verbose = verbose) - process.AllelicCrosstalkCalibration() is in environment Thanks Nitesh -- 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/
[aroma.affymetrix] Re: Error in getGenomeInformation
Henrik, thanks again. It's working now. On Monday, June 18, 2012 4:58:19 PM UTC-4, NT_CMU wrote: Hi I'm trying to run the command doCRMAv2, and i get these errors. Let me know what the problem is, if any of you have encountered this before. I thought i did not have some library installed but, i have both ACNE and aroma.affymetrix working properly. ds - doCRMAv2(LeeAV_2012,chipType=GenomeWideSNP_6,Full) Error in getGenomeInformation.AffymetrixCdfFile(cdf) : [2012-06-18 16:55:10] Exception: Failed to retrieve genome information for this chip type: GenomeWideSNP_6 at #12. getGenomeInformation.AffymetrixCdfFile(cdf) - getGenomeInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #11. getGenomeInformation(cdf) - getGenomeInformation() is in environment 'aroma.affymetrix' at #10. getSubsetToAvg.AllelicCrosstalkCalibration(this) - getSubsetToAvg.AllelicCrosstalkCalibration() is in environment 'aroma.affymetrix' at #09. getSubsetToAvg(this) - getSubsetToAvg() is in environment 'aroma.affymetrix' at #08. getParameters.AllelicCrosstalkCalibration(this) - getParameters.AllelicCrosstalkCalibration() is in environment 'aroma.affymetrix' at #07. getParameters(this) - getParameters() is in environment 'R.rsp' at #06. process.AllelicCrosstalkCalibration(acc, verbose = verbose) - process.AllelicCrosstalkCalibration() is in environment Thanks Nitesh -- 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/
[aroma.affymetrix] Re: Error in getGenomeInformation
I feel it might be better to post my question in this thread, as I have encountered the same error. I've downloaded ufl, ugp, and acs files from AROMA SNP6 webpage, and the Full cdf file from Affymetrix. And I still got the same kind error NT_CMU got for getGenomeInformation. Could you please give me a hint, where should I look for? Thanks! On Monday, June 18, 2012 4:58:19 PM UTC-4, NT_CMU wrote: Hi I'm trying to run the command doCRMAv2, and i get these errors. Let me know what the problem is, if any of you have encountered this before. I thought i did not have some library installed but, i have both ACNE and aroma.affymetrix working properly. ds - doCRMAv2(LeeAV_2012,chipType=GenomeWideSNP_6,Full) Error in getGenomeInformation.AffymetrixCdfFile(cdf) : [2012-06-18 16:55:10] Exception: Failed to retrieve genome information for this chip type: GenomeWideSNP_6 at #12. getGenomeInformation.AffymetrixCdfFile(cdf) - getGenomeInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #11. getGenomeInformation(cdf) - getGenomeInformation() is in environment 'aroma.affymetrix' at #10. getSubsetToAvg.AllelicCrosstalkCalibration(this) - getSubsetToAvg.AllelicCrosstalkCalibration() is in environment 'aroma.affymetrix' at #09. getSubsetToAvg(this) - getSubsetToAvg() is in environment 'aroma.affymetrix' at #08. getParameters.AllelicCrosstalkCalibration(this) - getParameters.AllelicCrosstalkCalibration() is in environment 'aroma.affymetrix' at #07. getParameters(this) - getParameters() is in environment 'R.rsp' at #06. process.AllelicCrosstalkCalibration(acc, verbose = verbose) - process.AllelicCrosstalkCalibration() is in environment Thanks Nitesh -- 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/
