User: b.nota

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b.nota300
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300
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Netherlands
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18 hours ago
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3 years, 5 months ago
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Posts by b.nota

<prev • 141 results • page 1 of 15 • next >
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Comment: C: File not found error when using dupRadar::analyzeDuprates
... Thank you, I will check the newest version. ...
written 13 days ago by b.nota300
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Comment: C: File not found error when using dupRadar::analyzeDuprates
... Thank you, I think it is the tilde (~) in my path name. I thought R would understand that. ...
written 14 days ago by b.nota300
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File not found error when using dupRadar::analyzeDuprates
... I am trying to use dupRadar on bam files, but get an Rsubread error. However, Rsubread is properly installed and no errors there. Is this a bug? Here my code: library(dupRadar) bamDuprm <- markDuplicates(dupremover="picard", bam="Sample01Aligned.sortedByCoord.out.bam", ...
rsubread dupradar written 15 days ago by b.nota300 • updated 13 days ago by Gordon Smyth34k
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Comment: C: Cannot retrieve DE genes from goana GO terms
... Yes, it was indeed. Because the rownames were also numbers no error occurred... Many thanks (again), we get other and correct results now. ...
written 26 days ago by b.nota300
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Comment: C: Cannot retrieve DE genes from goana GO terms
... Hi Aaron, thanks for your reply. I modified your code in order to get only the significant GO terms in data.frame, and also with gene symbol and GO description. But to give a simple example, I use exactly your code from https://support.bioconductor.org/p/69808/. > summary(decideTests(lrt)) ...
written 26 days ago by b.nota300
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Cannot retrieve DE genes from goana GO terms
... We have done a simple analysis in edgeR, to find significant DE genes between two groups, followed by GO analysis with goana. We tried to follow protocol/manual. After finding significant GO terms we would like to see which genes are in these GO terms. We found a post describing how to get the DE ge ...
limma edger goana written 26 days ago by b.nota300 • updated 26 days ago by Aaron Lun20k
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Comment: C: limma roast results not in accordance with barcodeplot
... Thanks (again) for your help, it's really appreciated. It was indeed the index that was not correct. I used for roast only the ensemble gene names of interest (which worked, but was not correct). With barcodeplot this index gave an error, which is why I used the index vector like in your example ind ...
written 3 months ago by b.nota300
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limma roast results not in accordance with barcodeplot
... I am trying to use limma roast, as advised in a previous post post. However, I have doubts about if it is correct what I am doing, since the barcodeplot gives a different picture of my results. I have an RNA-seq experiment analyzed with limma trend, and want to see if a signature of 48 genes (from a ...
limma roast written 3 months ago by b.nota300
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Comment: C: What does "level" argument mean in groupGO function (cluster profiler)?
... Thanks for your comment. So due to the complexity of the GO graph structure, it is probably not possible to find a level where all GO terms are given. I didn't realize it, thanks for your time. ...
written 3 months ago by b.nota300
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Comment: C: What does "level" argument mean in groupGO function (cluster profiler)?
... Thanks again, I understand what you mean. Sorry I gave you that impression. I was actually not asking about a simple hypergeometric test, I understand how to do that with this package. I thought I was clear about that in my question, but probably I was not. I was interested in getting all GO terms, ...
written 3 months ago by b.nota300

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Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to get duplicate IDs numbered?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Goseq analysis with Biocarta, Reactome, and NCI pathways?
Popular Question 13 months ago, created a question with more than 1,000 views. For Goseq analysis with Biocarta, Reactome, and NCI pathways?
Scholar 17 months ago, created an answer that has been accepted. For A: warning in R
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Scholar 2.3 years ago, created an answer that has been accepted. For A: warning in R
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Scholar 3.1 years ago, created an answer that has been accepted. For A: warning in R

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