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 • 293 results • page 1 of 30 • next >
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Answer: A: Python Module from Kim and Volsky (2005) PAGE: Parametric Analysis of Gene Set E
... FYI, since you ask at the Bioconductor forum: I know that the PAGE algorithm has been implemented in the package PGSEA. ...
written 6 days ago by Guido Hooiveld1.9k
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Comment: C: How does the org.Dm.eg.db package deal with NOT annotation qualifiers when anno
... For human few proteins the NOT qualifier is also used, but this is only for a small percentage (1281 out of 409697 entries). Whether this is taken into account in the annotation packages (org.Xx.eg.db or GO.db), and if so how, is a good question! I don't know....   > GAF <- read.delim(gzfil ...
written 14 days ago by Guido Hooiveld1.9k
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Comment: C: How does the org.Dm.eg.db package deal with NOT annotation qualifiers when anno
... Is the NOT qualifier not specific for D. melanogaster GO annotation? As someone working with human or mouse data, I have never heard of that GO qualifier before... I would suggest a little more explanation and some sample code/examples would help, especially for the BioC core members who generate th ...
written 14 days ago by Guido Hooiveld1.9k
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Comment: C: error in installing bioconductor
... The same command is working for me the moment I write this, so the problem is on your side, and not with the Bioconductor servers. So check again, check whether you can browse the internet at all, restart your PC, etc.... ...
written 15 days ago by Guido Hooiveld1.9k
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Answer: A: error in gcrma function
... This is indeed a typical error of having all available RAM exhausted. Two suggestions: - perform RMA normalization (instead of gcRMA) [celfiles.rma <- rma(celfiles)]; AFAIK RMA requires less memory. - if applicable, be sure to run the 64bits version of R. On 64 bit operating systems more memor ...
written 16 days ago by Guido Hooiveld1.9k
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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 weeks 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 weeks 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 weeks 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 6 weeks 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 6 weeks ago by Guido Hooiveld1.9k

Latest awards to Guido Hooiveld

Popular Question 5 weeks ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Supporter 11 months ago, voted at least 25 times.
Popular Question 11 months ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Popular Question 11 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Centurion 2.9 years ago, created 100 posts.

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