User: Mark W Kimpel

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Mark W Kimpel830
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Posts by Mark W Kimpel

<prev • 83 results • page 1 of 9 • next >
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problem updating packages importing the package "MASS"
... I went to update packages and discovered multiple packages that import or depend on MASS to have non-zero exit status. An example is the BioC package "multtest". I must confess that I don't remember what MASS does/did but I believe it was a CRAN package. When I went there, it wasn't there, nor is it ...
multtest written 8.5 years ago by Mark W Kimpel830 • updated 8.5 years ago by Sean Davis21k
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Answer: A: problem with biocLite("Biobase") -- results in looping of download
... Sorry took me a bit to get to this, was out of the office yesterday. The problem seems to only occur if I try to execute biocLite("Biobase") from within my .Rprofile OR if I have tried and failed with this, escaped, and then retry without rebooting R. If I completely leave it out of my .Rprofile it ...
written 8.5 years ago by Mark W Kimpel830
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problem with biocLite("Biobase") -- results in looping of download
... The code below results in a looping behavior with Biobase downloaded over and over again until escaped, then each downloaded instance (all in different temp folders) is installed. This behavior began about the time that R-2.9.0 was released, but I had been using R-devel prior to that without problem ...
biobase written 8.5 years ago by Mark W Kimpel830
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cannot access annotation from ExpressionSet in Bioc-Devel
... I have a function that has run well for several years and suddenly tonight it blew up, unable to access the annotation slot of an ExpressionSet. Does annotation(myExpressionSet) no longer work? Below is my output with my sessionInfo(). You will see that I am have an ExpressionSet with $annotation e ...
annotation go biobase limma written 8.7 years ago by Mark W Kimpel830 • updated 8.7 years ago by john seers IFR810
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question on GSEAlm
... I've been successfully using GSEAlm for purposes quite similar to the examples in the vignette without difficulty. Now I would like to apply this package to a list of summary statistics derived from a one-sample t-test of 6 Cohen's D measurements. My options would seem to be either modeling the CD m ...
gsealm written 8.9 years ago by Mark W Kimpel830
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Comment: C: confused about J-G statistic of GSEAlm
... Robert, Thank you for the explanation, it gives me a better understanding of what is going on. After reading you email, I realized that the big discrepancies in the observed t-stats that I noted were in fact do to a computational error on my part. If you look at my code, you will see that I forgot ...
written 9.0 years ago by Mark W Kimpel830
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confused about J-G statistic of GSEAlm
... I'm confused about how the J-G statistic of Jiang and Gentleman (2007) is calculated. To check the results I was getting, I calculated the statistic with my own code and came up with a very different answer to that obtained using gsealmPerm (which uses GSNormalize). Before proceeding to my code, I a ...
go gsealm written 9.0 years ago by Mark W Kimpel830 • updated 9.0 years ago by rgentleman5.5k
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using GSEAlm with GO geneSetCollections
... I'm using a specific Affy chipset that is supported by BioC (rat2302) and would like to use GSEAlm to indentify GO genesets of interest (p <0.05). I am only interested in the GO BP ontology and only want to use the terminal leaves. What is the most straightforward way to achieve this? I've read t ...
go affy gotools category gseabase gsealm written 9.0 years ago by Mark W Kimpel830 • updated 9.0 years ago by Dykema, Karl90
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problem with AnnotationDbi
... The code below, which produces the error message and sessionInfo which follow, was working last week but now is not. I got into this because I am having trouble with the Category package and wanted to rebuild my build of ragene10stv1.db package that Category was depending on. This build, which had g ...
chipname db0 affy category annotationdbi written 9.1 years ago by Mark W Kimpel830 • updated 9.1 years ago by Hervé Pagès ♦♦ 13k
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Comment: C: problem with Category package and custom annotationDbi
... myEGs has length of 400 and all are in MyGeneUniverse, checked with setdiff. at hospital with mother having surgery today, so will post reproducible example when I can. assume that myEGs should be lengthy, not sure how to post this, hence the reason I did not post already. suggestions? thanks Mark ...
written 9.1 years ago by Mark W Kimpel830

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