User: Guido Hooiveld

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Guido Hooiveld • 2.4k
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Wageningen University, Wageningen, the Netherlands
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11 years, 12 months ago
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Posts by Guido Hooiveld

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Is GCRMA normalization possible with oligo?
... I am updating my analysis pipeline for Affymetrix arrays, and would like to use the library `oligo` for the analysis of all types/generations of arrays. Until now I used the functionality of the library `affy` to normalize the 1st generation of arrays (those arrays including MM probes), and usually ...
normalization gcrma oligo affymetrix pd.moe430a written 12 days ago by Guido Hooiveld • 2.4k • updated 12 days ago by James W. MacDonald ♦ 49k
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Comment: C: Ensembl plants at annotationHub?
... Thanks! Meanwhile downloaded the file and everything is working fine.   ...
written 8 weeks ago by Guido Hooiveld • 2.4k
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Comment: C: Ensembl plants at annotationHub?
... Hi Johannes, Thanks for your offer! As far as I am concerned only an EnsDb for the latest genome info for Arabidopsis would do for now. (EnsemblPlants, release 41, Sept 2018, here). Thanks a lot for your help! Guido ...
written 8 weeks ago by Guido Hooiveld • 2.4k
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Ensembl plants at annotationHub?
... Hi, I am regularly using the annotationHub to retrieve/query the Ensembl-based gene annotations (ensembldb). This works fine for e.g human and mouse, but I now would like to obtain info made available through the Ensembl Plant database; specifically for Arabidopsis ( http://plants.ensembl.org/Arabi ...
arabidopsis thaliana annotationhub ensembl ensembldb plant written 8 weeks ago by Guido Hooiveld • 2.4k • updated 8 weeks ago by Johannes Rainer • 1.3k
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Comment: C: Error in get(cdfname, object 'mm430mmentrezgcdf' not found
... I cannot reproduce your error because in R-3.5.1 I cannot get version 10 of the custom CDF installed (due to a namespace error; see below), but apparently you could. > install.packages("http://bioconductor.org/packages/2.1/data/annotation/src/contrib/mm430mmentrezgcdf_10.0.0.tar.gz", type='sour ...
written 9 weeks ago by Guido Hooiveld • 2.4k
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Answer: A: Error in get(cdfname, object 'mm430mmentrezgcdf' not found
... You are calling the ReadAffy function with the wrong argument/name for the CDF. This should be mm430mmentrezg (and not Mm430_Mm_ENTREZG). Also no need to rename the slot that contains the CDF name.   Thus: library(affy) library(mm430mmentrezgcdf,lib.loc='/Library/Frameworks/R.framework/Versions/ ...
written 9 weeks ago by Guido Hooiveld • 2.4k
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Comment: C: gseaplot vertical line
... Which vertical line do you exactly refer to? See here for example of a gseaplot obtained from clusterProfiler. The calculations and interpretation of the scores can be found (among others) here (PathwayCommons) or here (at the GSEA webpage). ...
written 10 weeks ago by Guido Hooiveld • 2.4k
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Answer: C: Using microarray re-annotation to combine array and Chip-Seq data
... Please be informed that mapping of the probes to the GenCode mouse genome (release M19) has already been done by Manhong Dai from the MBNI group. The most recent version of these so-called Custom CDFs (i.e. v23) has just been released; see here and select one of the GenCode-based PdInfo (recommended ...
written 10 weeks ago by Guido Hooiveld • 2.4k
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Answer: A: Gene names for the Probes
... Check this thread here: https://support.bioconductor.org/p/89308/ ...
written 3 months ago by Guido Hooiveld • 2.4k
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Comment: C: how to find ensembl genes belonging to a GO category?
... Thanks for the pointers; got it working. ...
written 3 months ago by Guido Hooiveld • 2.4k

Latest awards to Guido Hooiveld

Scholar 7 weeks ago, created an answer that has been accepted. For A: clusterProfiler: Which GO version is used behind ?
Scholar 3 months ago, created an answer that has been accepted. For A: clusterProfiler: Which GO version is used behind ?
Popular Question 4 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 6 months ago, created a question with more than 1,000 views. For Design and contrast question limma (additive or nested or duplicateCorrelation())??
Popular Question 7 months ago, created a question with more than 1,000 views. For How to retrieve 'conservation score' sequence?
Popular Question 19 months ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Scholar 19 months ago, created an answer that has been accepted. For A: Queries around makeOrgPackageFromNCBI
Scholar 19 months ago, created an answer that has been accepted. For A: clusterProfiler: Which GO version is used behind ?
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 problem generating Chinese hamster txdb from GFF file
Popular Question 19 months ago, created a question with more than 1,000 views. For troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
Popular Question 19 months ago, created a question with more than 1,000 views. For minfi, bumphunter + complex experimental design, and 3 other 450K queries
Popular Question 19 months ago, created a question with more than 1,000 views. For package/function for median center & unit variance
Popular Question 19 months ago, created a question with more than 1,000 views. For limma: one sample t-test + covariate
Popular Question 19 months ago, created a question with more than 1,000 views. For Design and contrast question limma (additive or nested or duplicateCorrelation())??
Popular Question 19 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Taking surrogate variable into account before running PCA
Scholar 19 months ago, created an answer that has been accepted. For A: Taking surrogate variable into account before running PCA
Popular Question 19 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Testing for DE genes
Popular Question 23 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 2.8 years ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 2.8 years ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Supporter 2.8 years ago, voted at least 25 times.
Centurion 4.7 years ago, created 100 posts.
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