User: Ty Thomson
Ty Thomson • 100
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Posts by Ty Thomson
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... The problem ended up being caused by R studio. When I set R studio to no longer use IE settings it works! (Tools > Global Options > Packages, and unselect "Use Internet Explorer library/proxy for HTTP"; source: http://stackoverflow.com/questions/22721819/download-file-fails-in-rstudio)
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written 4.5 years ago by
Ty Thomson • 100
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... Hi Martin,
I tried sampleNames() as you suggested and it worked without error. But somehow in trying that I ended up using an R session outside of R studio. And my code above worked! So the problem that I'm encountering seems to be due to R studio. I had to use setInternet2(use = FALSE) to make ...
written 4.5 years ago by
Ty Thomson • 100
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... If I use getGEOSuppFiles() from the GEOquery package to download cel files directly from GEO, and in the same session try to run justRMA on those files, I sometimes get an error from justRMA:
Error in .Call("unsafe_set_slot", obj, slot, value) :
"unsafe_set_slot" not resolved from current namesp ...
written 4.5 years ago by
Ty Thomson • 100
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... Hi BioC List,
I'm working with an affymetrix data set where the batches are
completely confounded with the factor of interest for one contrast,
treatment time. From my understanding I can use something like fRMA
to partially mitigate the effect, but otherwise not much I can do.
However, we do hav ...
written 5.4 years ago by
Ty Thomson • 100
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... Hi Steve,
Thanks, that makes a lot of sense. I might just need to get another R
installation going so I can directly assess the effect of using all
the probes on my data.
Regards,
Ty
-----Original Message-----
From: Steve Piccolo [mailto:stephen.piccolo@hsc.utah.edu]
Sent: Tuesday, January 14, ...
written 5.9 years ago by
Ty Thomson • 100
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... Hi Steve,
Thanks for the suggestion. I'm running bioconductor 2.12 with
SCAN.UPC_2.0.2, and it doesn't look like this version of SCAN supports
the exonArrayTarget parameter. After reading the documentation for
the exonArrayTarget parameter in the most recent version of SCAN I
don't really underst ...
written 5.9 years ago by
Ty Thomson • 100
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... Hi Matt,
Thanks for the quick reply and the suggestions. I'll look into making
my own pd annotation and frmavecs packages.
Ty
-----Original Message-----
From: Matthew McCall [mailto:mccallm@gmail.com]
Sent: Monday, January 13, 2014 3:14 PM
To: Ty Thomson
Cc: bioconductor at r-project.org
Subjec ...
written 5.9 years ago by
Ty Thomson • 100
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... Apologies if any of my questions are naïve, as I don't have a lot of
experience with exon arrays. I would like to analyze an Affy HuGene
1.0 ST array using the brainArray CDF (because I want to get
expression values on a per gene level), and use fRMA (to correct for
batch effects and enable me to a ...
written 5.9 years ago by
Ty Thomson • 100
• updated
5.9 years ago by
Stephen Piccolo • 560
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... Hi Matt,
Updating to frmaTools_1.12.0 solved my problem. Thanks!
Ty
-----Original Message-----
From: Matthew McCall [mailto:mccallm@gmail.com]
Sent: Sunday, June 23, 2013 7:55 PM
To: Ty Thomson
Cc: bioconductor at r-project.org
Subject: Re: error in makeVectorsAffyBatch of frmaTools package
Ty, ...
written 6.5 years ago by
Ty Thomson • 100
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... Hi Matt (or anyone else who might be able to help),
I get an error when trying to run the makeVectorsAffyBatch() function
in the frmaTools package. I tried with an alternative cdf and I get
the same error. Any ideas? Thanks!
Ty
> require(frmaTools)
> files <- dir()
> x <- makeVe ...
written 6.5 years ago by
Ty Thomson • 100
• updated
6.5 years ago by
Matthew McCall • 830
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Popular Question
4.5 years ago,
created a question with more than 1,000 views.
For using frma and brainarray cdf on exon arrays
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