Hi,
this was due to a bug unrelated to writeSgr(). It's been patched.
Install the patch by:
library("aroma.affymetrix")
downloadPackagePatch("aroma.affymetrix")
Let us know if this works for you.
Cheers,
/Henrik
On Tue, Jun 23, 2009 at 10:31 AM, Josie Clowney<[email protected]> wrote:
> Hi Aroma,
> I'm using aroma to analyze custom affy tiling arrays. (Thanks for the MAT
> implementation!) Would like to write CEL files to IGB-viewable traces. The
> analysis seems to run fine, outputs CEL files that have data in them. The
> writeSgr command says "coming soon" and doesn't run:
>> writeSgr(csMS)
> Error in UseMethod("writeSgr") : no applicable method for "writeSgr"
> Is there a different method I can use in the meantime? Does anyone know what
> kind of file the Affy Power Tools command apt-summary-vis takes?
> Also, a more theoretical question, what does the MAT procedure do when it is
> smoothing and some of the genomic region in the probeWindow has no probes?
> For example most tiling arrays have many gaps due to repeat-masking. Will
> this cause edge effects in the smoothing of probes near the gap?
> Thanks for everything!
> Josie
> UCSF
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin8.11.1
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> other attached packages:
> [1] limma_2.18.1 aroma.affymetrix_1.1.0 aroma.apd_0.1.3
> R.huge_0.1.7
> [5] affxparser_1.16.0 aroma.core_1.1.0 aroma.light_1.13.2
> matrixStats_0.1.5
> [9] R.rsp_0.3.4 R.filesets_0.5.1 digest_0.3.1
> R.cache_0.1.7
> [13] R.utils_1.1.6 R.oo_1.4.6 R.methodsS3_1.0.3
> loaded via a namespace (and not attached):
> [1] affy_1.22.0 affyio_1.12.0 Biobase_2.4.1
> gsmoothr_0.1.1 marray_1.22.0
> [6] preprocessCore_1.6.0
>
>
>
> >
>
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