Anyone want to help me out by contributing the pd.mirna.4.1 package? I've used pdInfoBuilder for many of the rare arrays we have done in the past but apparently I'm not creative enough to make it work for this array. -- output of sessionInfo(): R version 3.1.0 (2014-04-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] pdInfoBuilder_1.28.0 oligo_1.28.0 Biostrings_2.32.0 [4] XVector_0.4.0 IRanges_1.22.6 oligoClasses_1.26.0 [7] affxparser_1.36.0 RSQLite_0.11.4 DBI_0.2-7 [10] Biobase_2.24.0 BiocGenerics_0.10.0 BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] affyio_1.32.0 bit_1.1-12 codetools_0.2-8 [4] compiler_3.1.0 ff_2.2-13 foreach_1.4.2 [7] GenomeInfoDb_1.0.2 GenomicRanges_1.16.3 iterators_1.0.7 [10] preprocessCore_1.26.0 splines_3.1.0 stats4_3.1.0 [13] tools_3.1.0 zlibbioc_1.10.0 -- Sent via the guest posting facility at bioconductor.org.

Hi CJ, For now you will have to use TAC instead of oligo. There are two changes that Affy made with the 4.X versions of the miRNA arrays (they are PM-only now, and they are recycling probes into multiple probesets) that oligo currently doesn't support. Fixing the first change is trivial. The second might be trivial as well, as this is the same issue that came up with the Gene ST arrays, so there is code in pdInfoBuilder to handle it. But that code applies to all of the Gene ST arrays, not just a subset, so that might make things a bit more complicated. Best, Jim On 5/10/2014 11:47 AM, Craig Johnson [guest] wrote: > Anyone want to help me out by contributing the pd.mirna.4.1 package? I've used pdInfoBuilder for many of the rare arrays we have done in the past but apparently I'm not creative enough to make it work for this array. > > > > -- output of sessionInfo(): > > R version 3.1.0 (2014-04-10) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] pdInfoBuilder_1.28.0 oligo_1.28.0 Biostrings_2.32.0 > [4] XVector_0.4.0 IRanges_1.22.6 oligoClasses_1.26.0 > [7] affxparser_1.36.0 RSQLite_0.11.4 DBI_0.2-7 > [10] Biobase_2.24.0 BiocGenerics_0.10.0 BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] affyio_1.32.0 bit_1.1-12 codetools_0.2-8 > [4] compiler_3.1.0 ff_2.2-13 foreach_1.4.2 > [7] GenomeInfoDb_1.0.2 GenomicRanges_1.16.3 iterators_1.0.7 > [10] preprocessCore_1.26.0 splines_3.1.0 stats4_3.1.0 > [13] tools_3.1.0 zlibbioc_1.10.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099