User: Guido Hooiveld

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

<prev • 288 results • page 1 of 29 • next >
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Comment: C: Annotating DEseq output using AnnotationDbi mapIds and most results say NA
... Thanks! Will go for the 1st option! ...
written 5 days ago by Guido Hooiveld1.9k
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Comment: C: Annotating DEseq output using AnnotationDbi mapIds and most results say NA
... Hi Johannes, Any chance you can make EnsDb.Mmusculus.v87 available through the Bioconductor annotation pages? Or any other way? For my data set I (also) would like to make use of the latest annotation info available. :) Thanks, Guido ...
written 5 days ago by Guido Hooiveld1.9k
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Comment: C: RNA degradation plot for GeneChip Mouse Gene 2.0 ST Array
... FWIW: after removing the NAs from the transcript-level probeset table (z), this code is also working nicely for mouse Gene ST1.1 arrays (pd.mogene.1.1.st.v1) Specifically; after the dbGetQuery (code box 2), and before making the GRanges object (box 3), add this line : z <- z[!is.na(z$start) | ...
written 5 days ago by Guido Hooiveld1.9k
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Comment: C: How to use brainarray custom cdf for HTA platform?
... If I filter my data set, which I usually do not, then most of the time I do this based on the IQR (interquartile range). See below for the signal distribution of my HTA2.0 data set (RMA normalized; RNA was from cell lines). http://imgur.com/BfcLLIl ...
written 9 days ago by Guido Hooiveld1.9k
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Comment: C: How to use brainarray custom cdf for HTA platform?
... Hi James, That's a good observation with some potential serious implications! Thanks for making me/us aware of this. Just to add my experience: first of all, I also don't know what the exact procedure is for Manhong when he generates these custom CDFs, and how he creates the CDF files themselves. ...
written 9 days ago by Guido Hooiveld1.9k
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Comment: C: How to use brainarray custom cdf for HTA platform?
... Recently I have analyzed a HTA2.0 array data set. Indeed, remapped PdInfo objects are not available for this (and some other) arrays. According to Manhong (maintainer of the Custom CDFs): "It is very slow to use BioC's built-in method to build those pdInfo packages, some of them even give me coredum ...
written 10 days ago by Guido Hooiveld1.9k
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Comment: C: clusterProfiler - enrichGO and enrichPathway not returning any results
... - What is the actual output of head(gene, 2)? It is certainly not what you show here.... Please also note that gene should be a character vector of  EntrezIDs. - What happens if you include the argument pvalueCutoff = 1 with enrichPathway(gene)? Maybe you don't have any significant results using th ...
written 20 days ago by Guido Hooiveld1.9k
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select function not working with annotation package; bug?
... I am analyzing some Illumina BeadArrays downloaded from GEO, but when annotating the results I noticed the select function can apparently not access all annotation information. I think this is a bug, but please correct me if this is intentional... The arrays are Sentrix Mouse-6 v1.1 arrays, and I u ...
annotation illuminamousev1p1.db annotationdata written 27 days ago by Guido Hooiveld1.9k • updated 27 days ago by James W. MacDonald42k
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Comment: C: convert data frame of Entrez IDs to Gene Symbols
... No, thanks; working nicely... for the archive: when rearranging the matrix with mapped results, be sure to use the correct number of rows (= same as your input). :) ...
written 4 weeks ago by Guido Hooiveld1.9k
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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 5 weeks ago by Guido Hooiveld1.9k

Latest awards to Guido Hooiveld

Popular Question 10 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 10 months ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Supporter 10 months ago, voted at least 25 times.
Centurion 2.8 years ago, created 100 posts.

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