[BioC] pd.mirna.4.1

[James W. MacDonald]

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.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099