User: Dykema, Karl

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Dykema, Karl90
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Last seen:
8 years, 5 months ago
Joined:
14 years, 3 months ago
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k**********@vai.org

Posts by Dykema, Karl

<prev • 8 results • page 1 of 1 • next >
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Illumina CanineHD CNV & crlmm?
... Dear Dr. Ritchie and Bioconductor users, Has anyone succeeded in loading data from the Illumina CanineHD CNV bead array into Bioconductor? I think the crlmm package is what I should use but there is no existing CDF for this array. I downloaded the annotations from the Illumina FTP site but I'm not ...
go cdf affy crlmm written 8.5 years ago by Dykema, Karl90
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Problem with ReadAffy and Connectivity Map .CEL files
... Hello all, I am having troubles reading in some CEL files from the Broad Connectivity Map. (http://www.broadinstitute.org/cmap/) Some of the files seem to work fine, but when I try to load a file with the chip type "HT_HG-U133A_EA" I receive me this error message: > ReadAffy(filenames=tf[1:2]) ...
written 9.5 years ago by Dykema, Karl90 • updated 9.5 years ago by James W. MacDonald50k
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Answer: A: Loading the PGSEA package.
... Marcus, ? Ruuid is only need for creating GSEAbase geneSetCollection objects so it shouldn't have been in the "Depends:" field in the first place! I moved it to "Suggests:" and committed my changes to the development version. Look for version 1.11.1 to show up here: ? http://bioconductor.org/package ...
written 10.3 years ago by Dykema, Karl90
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Answer: A: using GSEAlm with GO geneSetCollections
... Hello Mark, You may want to try PGSEA together with limma. It takes a slightly different approach than Category but this vignette should explain things adequately. http://www.bioconductor.org/packages/release/bioc/vignettes/PGSEA/inst /doc/PGSEA2.pdf ------------------------------------------- ...
written 10.5 years ago by Dykema, Karl90
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FW: How to plot microRNA chromosome location
... Hello Bioc users, While our package idiogram is has been created to primarily display gene expression data (with an associated chromLocation object) you can alternatively create one on the fly. In the code below I create a mock data frame similar to Camper's and from that I generate a bare ...
organism idiogram written 10.5 years ago by Dykema, Karl90
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Answer: A: ENTREZ identifiers for PGSEA
... Hi all, We have been having an offline discussion of this issue. I am posting the correspondence so that it can be referenced in the future. Thanks. -karl Sebastien, Nope, you are doing it exactly right. I fixed that problem a while ago but apparently neglected to upload my code changes to Bio ...
written 10.9 years ago by Dykema, Karl90
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exonmap package - MySQL error
... Bioc users - I am trying to set up the exonmap package and I have run into a problem that does not appear to be previously discussed in the mailing list. I have installed my local copy of Ensembl as well as the X-map database, as shown here. I can load exonmap library and the example data but I run ...
exonmap written 11.6 years ago by Dykema, Karl90
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Re: RMAGEML Package
... Hello, I am trying to use the RMAGEML package to read in some data from the EBI ArrayExpress database. However, when I try and use the importMAGEML() function, I get this error: Error in checkSlotAssignment(object, name, value) : Assignment of an object of class "list" is not valid for slot "maLab ...
rmageml written 14.3 years ago by Dykema, Karl90 • updated 14.3 years ago by Seth Falcon7.4k

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