User: Guido Hooiveld

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Guido Hooiveld2.2k
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Wageningen University, Wageningen, the Netherlands
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Posts by Guido Hooiveld

<prev • 344 results • page 2 of 35 • next >
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Answer: C: 'DESeqDataSetFromTximport' not found
... Please provide the output of sessionInfo()! The fuction is (at least) available when using R-3.4.x and Bioconductor v3.5. This will run DESeq2 v1.16.1, which thus contains the function DESeqDataSetFromTximport. See below for my SessionInfo(). <<edit>> The DESeq2 news file states that fr ...
written 23 days ago by Guido Hooiveld2.2k
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Answer: A: clusterProfiler: Which GO version is used behind ?
... AFAIK clusterProfiler uses under the hood the GO information available in the library GO.db. This GO annotation database is updated twice a year before each new Bioconductor release. Assuming you are using the latest Bioconductor release (i.e. 3.5), then the GO data was collected on 29 March 2017 (G ...
written 10 weeks ago by Guido Hooiveld2.2k
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Answer: A: Some questions about chip quality control
... In practice we almost never look at the values of these metrics as such, but rather look for samples that deviate from the majority. We then check whether e.g. pseudo-images indicate the presence of stains, or that some samples e.g. belong to a different tissue (e.g. liver versus intestine). In case ...
written 11 weeks ago by Guido Hooiveld2.2k
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Comment: C: oligo: crash/segfault when fitting probelevel model
... Thanks Ben for replying so promptly! As per your suggestion (and for completeness I also post this here): I have opened an issue on GitHub: https://github.com/bmbolstad/preprocessCore/issues/1 to which I also added some more information on my attempts to get it working. ...
written 12 weeks ago by Guido Hooiveld2.2k
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Comment: C: oligo: crash/segfault when fitting probelevel model
... Thanks James for your suggestion! But... no, reinstalling oligoData unfortunately did not solve it. RMA normalization just works fine?!?. See below. As said before, could it be that preprocessCore somehow is not working with a multi-threaded BLAS? However, I am not knowledgeable enough to show thi ...
written 12 weeks ago by Guido Hooiveld2.2k
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oligo: crash/segfault when fitting probelevel model
... A fresh Linux install of R crashes/segfaults when fitting a probelevel model using oligo on a dataset. Is this a bug? If not, any idea how to fix this? I don't know whether it is important, but please note that R is configured to use multi threaded OpenBLAS (rather than the default single-threaded B ...
oligo preprocesscore openblas written 12 weeks ago by Guido Hooiveld2.2k • updated 12 weeks ago by James W. MacDonald45k
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Comment: C: oligo and parallel computing (on Windows)?
... Thanks for your feedback. My take-home message: the above (still) is the proper way of using multiple cores with oligo, but the impact is indeed not impressive. ...
written 3 months ago by Guido Hooiveld2.2k
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oligo and parallel computing (on Windows)?
... I am about to get a large microarray data set which I would like to analyze using oligo. To run the analyses as efficiently as possible, I am exploring the parallelization options mentioned in the oligo user guide (section 7.3; Parallel Computing on Multicore Machines, pages 46-47). See also code be ...
oligo parallel computation written 3 months ago by Guido Hooiveld2.2k • updated 3 months ago by James W. MacDonald45k
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Comment: C: Error installing pd.huex.1.0.st.v2: database disk image is malformed
... <<EDIT>> I just noticed that the message No methods.... also popped up in your session. Apparently this is a warning, and not a (fatal) error, because I indeed could load the PdInfo package without problems (library("pd.hg.u133.plus.2")). I was too focused on all these messages, and didn ...
written 3 months ago by Guido Hooiveld2.2k
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Comment: C: Error installing pd.huex.1.0.st.v2: database disk image is malformed
... Mmm, something weird is going on... - I freshly installed (updated R to) R-3.4.1 (same as you, I was running R-3.4.0), and re-installed the latest RTools, but problem unfortunately remained...? - To exclude it may have something to do with relatively large size of the PdInfo package, I tried to in ...
written 3 months ago by Guido Hooiveld2.2k

Latest awards to Guido Hooiveld

Popular Question 5 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Scholar 5 months ago, created an answer that has been accepted. For A: Taking surrogate variable into account before running PCA
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Taking surrogate variable into account before running PCA
Popular Question 5 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Testing for DE genes
Popular Question 9 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 19 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 19 months ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Supporter 19 months ago, voted at least 25 times.
Centurion 3.5 years ago, created 100 posts.

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