User: Guido Hooiveld

gravatar for Guido Hooiveld
Guido Hooiveld2.3k
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Wageningen University, Wageningen, the Netherlands
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Joined:
11 years, 9 months ago
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Posts by Guido Hooiveld

<prev • 386 results • page 1 of 39 • next >
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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 1 day ago by Guido Hooiveld2.3k
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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 1 day ago by Guido Hooiveld2.3k
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Answer: A: Gene names for the Probes
... Check this thread here: https://support.bioconductor.org/p/89308/ ...
written 5 weeks ago by Guido Hooiveld2.3k
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Comment: C: how to find ensembl genes belonging to a GO category?
... Thanks for the pointers; got it working. ...
written 6 weeks ago by Guido Hooiveld2.3k
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how to find ensembl genes belonging to a GO category?
... Hi, I have a list of Gene Ontology IDs, and I would like to extract the genes (ensembl IDs) that belong to these GO terms. To do this I would like to use the biomaRt package. However, I cannot get it to work; i get an error indicating an invalid filter is used. This also happens when running an exa ...
go biomart gene ontology written 6 weeks ago by Guido Hooiveld2.3k • updated 6 weeks ago by James W. MacDonald48k
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Comment: C: OrgDb for Tetrahymena thermophila
... Well, the above line of code (still) works for me on the current version of R/BioC... (although run-time was longer than before [now ~20hrs]). If needed, I can sent you the OrgDb library I made. ># set working dir to a location with sufficient HDD space ># needed >35GB >setwd("D:\\my ...
written 7 weeks ago by Guido Hooiveld2.3k
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Answer: A: Deseq: What does "BaseMean" mean?
... "The first column, baseMean, is a just the average of the normalized count values, dividing by size factors, taken over all samples." See e.g. Mike's workflow published at the F1000 here (section "Building the results table").   ...
written 8 weeks ago by Guido Hooiveld2.3k
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Comment: C: ensembldb salmon deseq2 txt2import right tool?
... FYI: Johannes' solution is automagically performed within the tximport function when specifying the argument ignoreTxVersion = TRUE (default = FALSE). ...
written 8 weeks ago by Guido Hooiveld2.3k
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Comment: C: Using Limma to normalize data sets
... at the help page of ReadAffy (found by ?ReadAffy) find the option 'compress': compress: are the CEL files compressed?   Thus (assuming the last file in your list (GSM1293830_19_10_Control_108h.CE) has a wrong extension because of an incomplete copy/paste error): AffyData <- ReadAffy(filenam ...
written 10 weeks ago by Guido Hooiveld2.3k
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Comment: C: No gene can be mapped error with clusterprofiler
... Your code is working for me. I used as input the 12 UMA IDs above. Although not directly related to the problem your reported, please note that the function enrichKEGG() is used to check which KEGG pathways are over-represented in a list of selected genes, e.g. identified by an differential gene ex ...
written 11 weeks ago by Guido Hooiveld2.3k

Latest awards to Guido Hooiveld

Popular Question 10 weeks ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 3 months ago, created a question with more than 1,000 views. For Design and contrast question limma (additive or nested or duplicateCorrelation())??
Popular Question 5 months ago, created a question with more than 1,000 views. For How to retrieve 'conservation score' sequence?
Scholar 16 months ago, created an answer that has been accepted. For A: clusterProfiler: Which GO version is used behind ?
Scholar 16 months ago, created an answer that has been accepted. For A: Queries around makeOrgPackageFromNCBI
Popular Question 16 months ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Popular Question 16 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 16 months ago, created a question with more than 1,000 views. For problem generating Chinese hamster txdb from GFF file
Popular Question 16 months ago, created a question with more than 1,000 views. For minfi, bumphunter + complex experimental design, and 3 other 450K queries
Popular Question 16 months ago, created a question with more than 1,000 views. For package/function for median center & unit variance
Popular Question 16 months ago, created a question with more than 1,000 views. For limma: one sample t-test + covariate
Popular Question 16 months ago, created a question with more than 1,000 views. For Design and contrast question limma (additive or nested or duplicateCorrelation())??
Popular Question 16 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Taking surrogate variable into account before running PCA
Scholar 17 months ago, created an answer that has been accepted. For A: Taking surrogate variable into account before running PCA
Popular Question 17 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: Testing for DE genes
Popular Question 21 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 2.6 years ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Popular Question 2.6 years ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Supporter 2.6 years ago, voted at least 25 times.
Centurion 4.5 years ago, created 100 posts.

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