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
--~--~---------~--~----~------------~-------~--~----~
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.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
aroma-affymetrix-unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
-~----------~----~----~----~------~----~------~--~---
