User: Fraser Sim

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Fraser Sim270
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Posts by Fraser Sim

<prev • 27 results • page 1 of 3 • next >
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Comment: C: Farms/Call.INI using oligo package?
... Dear Okko, Thanks! This function worked and I am able to call INIcalls and getI_ProbeSets on my affyExpressionFS object. What is a little odd is that I’m only getting 4836 features that pass, out of 53617 on the hugene2.0st on the entire array. I realize you said that call filter would not wor ...
written 6.1 years ago by Fraser Sim270
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Farms/Call.INI using oligo package?
... Hi, I am analyzing Affymetrix hugene2.0st arrays using the oligo package and had hoped to be able to use informative/non-informative probe calling (FARMS, Tolloen et 2007) as a means on filtering data. I had used this on older 3' biased arrays analyzed with affy but the farms package only works w ...
probe affy oligo farms written 6.1 years ago by Fraser Sim270 • updated 6.1 years ago by Djork Clevert210
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Comment: C: CDF for GeneChip miRNA 2 array - Is there a miRNA 3 CDF?
... Hi Jim, Thanks for the quick response. I called Affy and they will send me the CDF file so that I can build my own. I asked about public availability and the tech support person told me that the request to be made public was submitted and is currently being discussed. So hopefully they will put it ...
written 7.4 years ago by Fraser Sim270
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CDF for GeneChip miRNA 2 array - Is there a miRNA 3 CDF?
... Hi, Is there a BioC-compatible CDF file for miRNA 3.0 Arrays? I'm getting "mirna30cdf not available" error message when trying to run justRMA(). Cheers, Fraser -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Hooiveld ...
mirna annotation cdf written 7.4 years ago by Fraser Sim270 • updated 7.4 years ago by James W. MacDonald52k
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Comment: C: limma report logFC confidence interval?
... Hi Gordon, I agree. This would be useful addition as some readers, especially non-statisticians, would like to see the relative errors of the logFCs on plots and tables. Cheers, Fraser -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces at r-project.or ...
written 8.9 years ago by Fraser Sim270
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Comment: C: Rgraphviz in windows 7 - problem with GUI?
... Hi Grace, It looks like you're using an old version of R. You should upgrade to 2.12.1. What version of graphviz do you have installed? What happens when you run "library(Rgraphviz)"? Cheers, Fraser -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces ...
written 9.0 years ago by Fraser Sim270
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Comment: C: Rgraphviz in windows 7 - problem with GUI?
... Are you able to run graphviz without a crash? i.e. go to start menu > programs > graphviz > dotty.exe It sounds like you have an incompatible version of graphviz installed. I know 64-bit Windows requires a newish version to work correctly. Cheers, Fraser -----Original Message----- From: ...
written 9.0 years ago by Fraser Sim270
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Answer: A: core bioconductor packages
... Follow instructions at: http://www.bioconductor.org/install/ -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Pradeep Battula Sent: Friday, November 05, 2010 10:35 AM To: bioconductor at stat.math.ethz.ch Subject ...
written 9.1 years ago by Fraser Sim270
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building annotation package for porcine
... Dear Marc, I tried to run your suggested code to generate a porcine annotation package in 2.12.0 (64-bit). However it returns a cryptic error message. Any help would be most appreciated. (The csv file was downloaded from NetAffx today.) Cheers, Fraser > library(AnnotationDbi) > makeDBPackag ...
annotation cancer chipname genefilter limma annotationdbi written 9.1 years ago by Fraser Sim270 • updated 9.1 years ago by Marc Carlson7.2k
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Comment: C: Interrupting an R command
... Answering my own post. I found a page http://www.stats.ox.ac.uk/~ripley/Win64/W64porting.html which has a link to a 64-bit abridged version of graphviz which has been built for 64-bit windows. Here's how I installed the package: 1. Extracted the acrhive (http://www.stats.ox.ac.uk/pub/Rtools/goodies ...
written 9.1 years ago by Fraser Sim270

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