User: Guido Hooiveld

gravatar for Guido Hooiveld
Guido Hooiveld2.2k
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Wageningen University, Wageningen, the Netherlands
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Joined:
11 years ago
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Posts by Guido Hooiveld

<prev • 354 results • page 1 of 36 • next >
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Comment: C: problem using AnnotationDbi
... Based on this error:  there is no package called ‘digest’, it likely means you have to install the package digest first. source("https://bioconductor.org/biocLite.R") biocLite("digest")   ...
written 12 days ago by Guido Hooiveld2.2k
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Comment: C: Microarray analysis using RMA method using affy, limma
... The workflow at F1000 may also be a good place to start. ...
written 20 days ago by Guido Hooiveld2.2k
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Comment: C: limma package for DEGs analysis
... Please be more specific by providing the output of the function that apparently is not doing what you expect it do do, because "it is not working" is not really informative... and people don't have the time to reproduce your lines of code without having access to the raw data. In addition, please r ...
written 26 days ago by Guido Hooiveld2.2k
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Comment: C: how to reformat complex list object (derived with TCGAbiolinks)?
... Hi. I am not so familiar with all the data formats present at TCGA, so initially I expected the output for the 'isoform' data also to be a count-based table (like for the precursor data that I first generated). However, due to the differences in rows I now understand all data is just appended to for ...
written 4 weeks ago by Guido Hooiveld2.2k
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Comment: C: how to reformat complex list object (derived with TCGAbiolonks)?
... For completeness the code that was used to generate the object data above: library(TCGAbiolinks) library(dplyr) library(DT) library(SummarizedExperiment) # project: TCGA-LIHC # isoforms (data.type = "Isoform Expression Quantification") query <- GDCquery(project = c("TCGA-LIHC"), ...
written 5 weeks ago by Guido Hooiveld2.2k
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how to reformat complex list object (derived with TCGAbiolinks)?
... I face a problem with the output of the package TGCAbiolinks. My ultimate goal is to reanalyze the miRNA isoform data from the TCGA-LIHC project (data.type = "Isoform Expression Quantification"). I used the library TGCAbiolinks to download this dataset from the TCGA repository. The problem is that I ...
tcga list tcgabiolinks reformat written 5 weeks ago by Guido Hooiveld2.2k
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Answer: A: How to use custom cdf "hgu133plus2hsentrezgcdf"?
... The remapped, custom CDFs can not be downloaded using BiocLite(); you rather have to download them directly from the MBNI group website. As an example, assuming you are on windows and would like to use the latest version (=v22) of the custom CDFs: install.packages("http://mbni.org/customcdf/22.0. ...
written 6 weeks ago by Guido Hooiveld2.2k
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Comment: C: Error in Expression File Creator
... Which Bioconductor package are you using? Could you please provide your full code? Expression File Creator is (also) a module of GenePattern from the Broad Institute, and this apparently is not compatible with the new generation of Affymetrix arrays: http://software.broadinstitute.org/cancer/softwa ...
written 10 weeks ago by Guido Hooiveld2.2k
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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 12 weeks 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 12 weeks ago by Guido Hooiveld2.2k • updated 12 weeks ago by Gordon Smyth32k

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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