User: Guido Hooiveld

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Guido Hooiveld2.3k
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Wageningen University, Wageningen, the Netherlands
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Posts by Guido Hooiveld

<prev • 379 results • page 1 of 38 • next >
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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 1 day 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 13 days 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 19 days ago by Guido Hooiveld2.3k
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Comment: C: enrichMKEGG can not identify the species
... Mmm, looks like you have a mix of release and development packages.... For R-3.5.x / Bioc-3.7 you should use clusterProfiler version 3.8.1 (here) (2nd number = an even number) , you have version 3.9.1 (2nd number = an odd number, thus the 'development' version). Maybe this explains your error; again ...
written 8 weeks ago by Guido Hooiveld2.3k
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Comment: C: Guidance to handle .CEL file in R
... To add to Bioconductor workflows linked to by Lori: the Affymetrix workflow at the F1000 here is also a good starter; for online QC analysis ArrayAnalysis.org might be handy. ...
written 8 weeks ago by Guido Hooiveld2.3k
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Answer: A: enrichMKEGG can not identify the species
... You did not define the object de, which you used as input. Also, the last line of your code is weird; why do you include head(summary(xx))?   Example from vignette is running fine for me (please note my comments): > library(clusterProfiler) > data(geneList, package='DOSE') > de <- na ...
written 8 weeks ago by Guido Hooiveld2.3k
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Comment: C: Error in Annotation Forge, makeOrgPackage
... Did you prepare the input files yourselves? I.e. fSym, fChr, and fGO? Could you show the content of these files using head()? How did you conclude that it didn't work? Could you show some code and sessionInfo()?   As a side note: please be informed that through the AnnotationHub a pre-made OrgDb ...
written 8 weeks ago by Guido Hooiveld2.3k
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Comment: C: Differences in gene length passed to DESeq2 by tximport reulted in different gen
... I just noticed that in Salmon version 0.11.0 a fix has been applied to correct a bug that for multi-isoform genes resulted in the wrong calculation of lengths and effective lengths of genes. Although this was, according to the release notes, (apparently) *only* an issue when these numbers were calcu ...
written 9 weeks ago by Guido Hooiveld2.3k
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Comment: C: Pathview results interpretation
... It would have been helpful if you also posted your code and/or graph, because now we have to *assume* the things you did... Anyway, if I plot/overlay my gene expression data using pathview, rectangles correspond indeed to genes/enzymes. If you plot fold changes, red is 'increased', and green is 'dec ...
written 3 months ago by Guido Hooiveld2.3k
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Comment: C: Affe package mas5 error
... It's working fine for me using some similar old (1st generation) mouse arrays that I had at hand. However, I noticed that you are using version 18 of the custom CDF, which was released more than 4 years ago.... Maybe these old CDFs are not compatible anymore with the current version of R/BioC? The ...
written 3 months ago by Guido Hooiveld2.3k

Latest awards to Guido Hooiveld

Popular Question 3 months ago, created a question with more than 1,000 views. For How to retrieve 'conservation score' sequence?
Scholar 14 months ago, created an answer that has been accepted. For A: clusterProfiler: Which GO version is used behind ?
Scholar 14 months ago, created an answer that has been accepted. For A: Queries around makeOrgPackageFromNCBI
Popular Question 14 months ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Popular Question 14 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 14 months ago, created a question with more than 1,000 views. For problem generating Chinese hamster txdb from GFF file
Popular Question 14 months ago, created a question with more than 1,000 views. For minfi, bumphunter + complex experimental design, and 3 other 450K queries
Popular Question 14 months ago, created a question with more than 1,000 views. For package/function for median center & unit variance
Popular Question 14 months ago, created a question with more than 1,000 views. For limma: one sample t-test + covariate
Popular Question 14 months ago, created a question with more than 1,000 views. For Design and contrast question limma (additive or nested or duplicateCorrelation())??
Popular Question 15 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Scholar 15 months ago, created an answer that has been accepted. For A: Taking surrogate variable into account before running PCA
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Taking surrogate variable into account before running PCA
Popular Question 15 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Testing for DE genes
Popular Question 19 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 2.4 years ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Popular Question 2.4 years ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Supporter 2.4 years ago, voted at least 25 times.
Centurion 4.3 years ago, created 100 posts.

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