User: b.nota

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b.nota320
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Netherlands
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6 days, 14 hours ago
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4 years, 2 months ago
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Posts by b.nota

<prev • 143 results • page 1 of 15 • next >
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Comment: C: How to calculate average log2 CPM with batch effect?
... That's a great solution! Thanks for explaining it so clearly. ...
written 6 months ago by b.nota320
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How to calculate average log2 CPM with batch effect?
... I have used limma trend to find DE genes between 3 groups (including batch effect in design). Now I would like to visualize the genes, and used removeBatchEffect() to get corrected logCPM values for each sample. logCPMc <- removeBatchEffect(logCPM, batch=targets$Batch, design=design_4_batch) No ...
limma edger cpm written 6 months ago by b.nota320 • updated 6 months ago by Aaron Lun23k
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Comment: C: File not found error when using dupRadar::analyzeDuprates
... Thank you, I will check the newest version. ...
written 8 months ago by b.nota320
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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 8 months ago by b.nota320
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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 8 months ago by b.nota320 • updated 8 months ago by Gordon Smyth37k
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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 9 months ago by b.nota320
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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 9 months ago by b.nota320
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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 9 months ago by b.nota320 • updated 9 months ago by Aaron Lun23k
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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 11 months ago by b.nota320
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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 11 months ago by b.nota320

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Popular Question 10 months ago, created a question with more than 1,000 views. For How to get duplicate IDs numbered?
Popular Question 10 months ago, created a question with more than 1,000 views. For Goseq analysis with Biocarta, Reactome, and NCI pathways?
Popular Question 22 months ago, created a question with more than 1,000 views. For Goseq analysis with Biocarta, Reactome, and NCI pathways?
Scholar 2.1 years ago, created an answer that has been accepted. For A: warning in R
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