User: Guido Hooiveld

gravatar for Guido Hooiveld
Guido Hooiveld2.3k
Reputation:
2,340
Status:
Trusted
Location:
Wageningen University, Wageningen, the Netherlands
Scholar ID:
Google Scholar Page
Last seen:
2 days, 20 hours ago
Joined:
11 years, 10 months ago
Email:
g*************@wur.nl

Posts by Guido Hooiveld

<prev • 391 results • page 2 of 40 • next >
0
votes
1
answers
378
views
1
answers
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 11 weeks ago by Guido Hooiveld2.3k
0
votes
1
answers
151
views
1
answers
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 11 weeks ago by Guido Hooiveld2.3k
0
votes
2
answers
577
views
2
answers
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 11 weeks ago by Guido Hooiveld2.3k
0
votes
1
answers
254
views
1
answers
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 3 months ago by Guido Hooiveld2.3k
0
votes
1
answers
1.2k
views
1
answers
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 3 months ago by Guido Hooiveld2.3k
0
votes
1
answers
218
views
1
answers
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 4 months ago by Guido Hooiveld2.3k
0
votes
0
answers
150
views
0
answers
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 4 months ago by Guido Hooiveld2.3k
0
votes
1
answers
218
views
1
answers
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 4 months ago by Guido Hooiveld2.3k
0
votes
1
answers
174
views
1
answers
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 4 months ago by Guido Hooiveld2.3k
0
votes
1
answers
349
views
1
answers
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 4 months ago by Guido Hooiveld2.3k

Latest awards to Guido Hooiveld

Scholar 6 weeks ago, created an answer that has been accepted. For A: clusterProfiler: Which GO version is used behind ?
Popular Question 3 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 4 months ago, created a question with more than 1,000 views. For Design and contrast question limma (additive or nested or duplicateCorrelation())??
Popular Question 6 months ago, created a question with more than 1,000 views. For How to retrieve 'conservation score' sequence?
Popular Question 17 months ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Scholar 17 months ago, created an answer that has been accepted. For A: Queries around makeOrgPackageFromNCBI
Scholar 17 months ago, created an answer that has been accepted. For A: clusterProfiler: Which GO version is used behind ?
Popular Question 17 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 17 months ago, created a question with more than 1,000 views. For problem generating Chinese hamster txdb from GFF file
Popular Question 17 months ago, created a question with more than 1,000 views. For minfi, bumphunter + complex experimental design, and 3 other 450K queries
Popular Question 17 months ago, created a question with more than 1,000 views. For package/function for median center & unit variance
Popular Question 17 months ago, created a question with more than 1,000 views. For limma: one sample t-test + covariate
Popular Question 17 months ago, created a question with more than 1,000 views. For Design and contrast question limma (additive or nested or duplicateCorrelation())??
Popular Question 17 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 18 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Commentator 19 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 import DOT (GraphViz) into Cytoscape
Supporter 2.6 years ago, voted at least 25 times.
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
Centurion 4.6 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 241 users visited in the last hour