User: Guido Hooiveld

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Guido Hooiveld1.9k
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Wageningen University, Wageningen, the Netherlands
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Posts by Guido Hooiveld

<prev • 279 results • page 1 of 28 • next >
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Comment: C: Custom cdf and Ensemble
... Check "Data Sources" for each version; you will then see that no version is based on Ensembl version 73, but the Ensembl-based v18 of the custom CDF is based on version 74.   ...
written 7 hours ago by Guido Hooiveld1.9k
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Comment: C: convert data frame of Entrez IDs to Gene Symbols
... @Aaron and Leandro, Thanks for your replies. Although both suggestions do work, it doesn't work for my use case (which turned out not to be sufficiently clear): I would like to get back the same data frame/matrix, but with the IDs replaced by the corresponding Symbols. Both your suggestions "only" ...
written 1 day ago by Guido Hooiveld1.9k
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convert data frame of Entrez IDs to Gene Symbols
... I am struggling with likely a simple problem, but I can't get it to work... I would appreciate if one of the more knowledgeable people could provide some code/directions to get it working... Thanks, Guido   I have a data frame consisting of human Entrez IDs, which I would like to convert into Gen ...
annotation written 2 days ago by Guido Hooiveld1.9k • updated 1 day ago by James W. MacDonald41k
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Comment: C: How to use brainarray custom cdf with oligo package?
... There is no need to make an annotation package yourselves for the remapped/custom/brainarray "CDF" when using oligo, because the annotations are already available in the remapped PdInfo object. <<edit: i was not completely correct; as James pointed out below, you still/also need the *.db file ...
written 6 days ago by Guido Hooiveld1.9k
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Comment: C: Help with error: 'pd.u133aaofav2 was not found in the BioConductor repository'.
... FYI: 'U133AAofAv2' apparently refers to the HT-U133A arrays of that dataset. The names of the required Platform Design packages are automagically inferred from the cell files. Since the names thus refer to a design which name has been superseded (see below), you need to explicitly state the PD packa ...
written 4 weeks ago by Guido Hooiveld1.9k
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Comment: C: Pre-processing of HTA 2.0 array
... Well, James basically explained it all in his answer above... Please note that by summarizing at the transcript or probeset level your are NOT analyzing on the level of genes! Hence a gene is thus expected to be represented by multiple transcripts (or probesets), exactly as you found. The discussion ...
written 7 weeks ago by Guido Hooiveld1.9k
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Comment: C: Accessing feature data of a Malus domestica Nimblegen microarray
... First of all, I don't know anything on the organism you are investigating. However, using a simple Google search I found this site (@ rosaceae) https://www.rosaceae.org/species/malus/malus_spp/unigene_v4 , which seems to contain (a little) more annotation info for the v4 release. That is, at the dow ...
written 7 weeks ago by Guido Hooiveld1.9k
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Comment: C: platform design package for new Clariom S arrays
... I don't have experience with these new arrays (yet), but I recall a recent thread on the "D" arrays on this site: https://support.bioconductor.org/p/86866/#86887   Bottom line: James proves some lines of code to generate such PlatformDesign package (for the human "D" array) using the files availa ...
written 8 weeks ago by Guido Hooiveld1.9k
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Answer: A: Issue of clusterprofiler package
... From experience I also know clusterProfiler and related packages are indeed frequently updated to add new functionality, which IMHO is very nice. As a result the use of functions and their arguments are sometimes changed. I agree with you that the example code on the help page of ?enrichGO doesn't ...
written 8 weeks ago by Guido Hooiveld1.9k
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Answer: A: Error in .testForValidKeys "org.Rn.eg.db"
... Your t1 vector contains HUMAN Ensembl IDs! Hence they keys are invalid for the rat database. Rat genes look like this: ENSRNOG00000018126 (Abca1). For your genes you should use the org.Hs.eg.db.   > library(org.Hs.eg.db) > t1 <- c( "ENSG00000000003", "ENSG00000000971", "ENSG00000001084" ...
written 8 weeks ago by Guido Hooiveld1.9k

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