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 • 356 results • page 2 of 36 • next >
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Answer: A: Error with ecolik12 enrichGO
... Please check the help page for the function enrichGO (type: ?enrichGO). You will then see that the 2nd argument should be OrgDb (and NOT organism), which is an genome-wide annotation library for an organism; in your case this should be "org.EcK12.eg.db". You can find this library here at the annot ...
written 3 months ago by Guido Hooiveld2.2k
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voomWithQualityWeights: question on min. number of replicates per group + design to use
... I have an RNA-seq data set (8 treatments, 2 replicates) that I would like to process by voom transformation for analysis in limma. I also would like to include sample-specific quality weights, so I know using the function voomWithQualityWeights() is the way to go. However, since I have only 2 repli ...
limma edger voom limma-voom voomwithqualityweights written 3 months ago by Guido Hooiveld2.2k • updated 3 months ago by Gordon Smyth32k
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Answer: A: How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
... This works exactly the same as for the mogene 2.0 ST arrays, which you asked before here.... 1) Guideline: prefer a ChipDb annotation package over a PdInfo package. 2) Check the Bioconductor annotationDb webpage here for the platform you are using; you will find this page: Affymetrix Human Genome ...
written 3 months ago by Guido Hooiveld2.2k
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Comment: C: GSEA using clusterProfiler
... I always use the limma output (which is of class MArrayLM) directly by subsetting/extracting the contrast of interest. It should work very similar when having your data in a data frame.   #check comparisons/contrasts that were made (and are stored in the fit object) colnames(fit2$contrasts) #[1] ...
written 3 months ago by Guido Hooiveld2.2k
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Comment: C: GSEA using clusterProfiler
... Please specify how you prepared the data you would like to use. ...
written 3 months ago by Guido Hooiveld2.2k
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Comment: C: How to annotate the [MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array chip
... Mmm, you also need to explore things yourselves a bit... XR is one of the 9 RefSeq annotation categories; the abbreviation XR is used to describe a 'predicted ncRNA model' that has been given the (numerical) ID 398539. Please note that this is a computational prediction, so no experimental evidence ...
written 3 months ago by Guido Hooiveld2.2k
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Answer: A: clusterProfiler compareCluster enrichDAVID
... 1): These are indeed based on significance. See also this post of Guangchuang. http://guangchuangyu.github.io/2016/11/showcategory-parameter-for-visualizing-comparecluster-output/   2): AFAIK the number of genes in each cluster.   3): I am sorry, but I don't know. (I don't use R studio).   ...
written 3 months ago by Guido Hooiveld2.2k
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Comment: C: How to annotate the [MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array chip
... Well, I don't fully agree with you. Your annotation 'problem' HAS been solved, because SYMBOLs and GENENAMEs were retrieved and added to your output. I agree with you regarding the many NA's that are present. However, this has (solely) to do with the limited annotation information Affymetrix provide ...
written 3 months ago by Guido Hooiveld2.2k
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Answer: A: How to annotate the [MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array chip
... Most convenient would be using the function annotateEset() from the package affycoretools. Use as input the (your) normalized object eset. You can then annotate your dataset using either the corresponding pdInfo package, or the ChipDb package. The annotation info available in the PdInfo package is ...
written 3 months ago by Guido Hooiveld2.2k
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Comment: C: GeneList issue ClusterProfiler
... One more thing: I noticed that your input list is relatively small (~550 genes). I think GSE(A) analysis on such small list is not useful, but that you rather should perform an over-representation analysis (ORA) with e.g. the function enrichKEGG (when wanting to use info from the KEGG database).   ...
written 3 months ago by Guido Hooiveld2.2k

Latest awards to Guido Hooiveld

Popular Question 8 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Scholar 8 months ago, created an answer that has been accepted. For A: Taking surrogate variable into account before running PCA
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Taking surrogate variable into account before running PCA
Popular Question 8 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Testing for DE genes
Popular Question 12 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 22 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 22 months ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Supporter 22 months ago, voted at least 25 times.
Centurion 3.8 years ago, created 100 posts.

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