User: Ty Thomson

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Ty Thomson100
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Posts by Ty Thomson

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Answer: A: namespace problem running GEOquery and justRMA in same session
... 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) ...
written 4.5 years ago by Ty Thomson100
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Comment: C: namespace problem running GEOquery and justRMA in same session
... 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 Thomson100
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namespace problem running GEOquery and justRMA in same session
... 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 ...
affy geoquery written 4.5 years ago by Ty Thomson100
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dealing with counfounded effects in experiment design
... 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 Thomson100
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Comment: C: using frma and brainarray cdf on exon arrays
... 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 Thomson100
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Comment: C: using frma and brainarray cdf on exon arrays
... 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 Thomson100
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Comment: C: using frma and brainarray cdf on exon arrays
... 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 Thomson100
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using frma and brainarray cdf on exon arrays
... 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 ...
cdf affy process oligo xps frma written 5.9 years ago by Ty Thomson100 • updated 5.9 years ago by Stephen Piccolo560
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Comment: C: error in makeVectorsAffyBatch of frmaTools package
... 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 Thomson100
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error in makeVectorsAffyBatch of frmaTools package
... 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 ...
cdf frmatools written 6.5 years ago by Ty Thomson100 • updated 6.5 years ago by Matthew McCall830

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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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