User: b.nota

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b.nota340
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Netherlands
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2 weeks, 6 days ago
Joined:
4 years, 9 months ago
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Posts by b.nota

<prev • 144 results • page 1 of 15 • next >
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limma::avereps for median?
... Hi, I am using Agilent single channel data and found the `limma::avereps` function handy, since the number of replicate probes on the array vary per gene (locus). However, I would prefer to have **median** in stead of averages. Is there a possibility (argument setting) to use this function to get th ...
limma written 24 days ago by b.nota340 • updated 23 days ago by Gordon Smyth39k
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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 14 months ago by b.nota340
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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 14 months ago by b.nota340 • updated 14 months ago by Aaron Lun25k
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Comment: C: File not found error when using dupRadar::analyzeDuprates
... Thank you, I will check the newest version. ...
written 16 months ago by b.nota340
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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 16 months ago by b.nota340
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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 16 months ago by b.nota340 • updated 16 months ago by Gordon Smyth39k
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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 16 months ago by b.nota340
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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 16 months ago by b.nota340
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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 16 months ago by b.nota340 • updated 16 months ago by Aaron Lun25k
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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 19 months ago by b.nota340

Latest awards to b.nota

Popular Question 12 months ago, created a question with more than 1,000 views. For Goseq analysis with Biocarta, Reactome, and NCI pathways?
Popular Question 12 months ago, created a question with more than 1,000 views. For Limma voom or trend?
Popular Question 12 months ago, created a question with more than 1,000 views. For Postdoc bioinformatics in proteomics
Popular Question 18 months ago, created a question with more than 1,000 views. For How to get duplicate IDs numbered?
Popular Question 18 months ago, created a question with more than 1,000 views. For Goseq analysis with Biocarta, Reactome, and NCI pathways?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Goseq analysis with Biocarta, Reactome, and NCI pathways?
Scholar 2.8 years ago, created an answer that has been accepted. For A: warning in R
Centurion 2.8 years ago, created 100 posts.
Supporter 3.6 years ago, voted at least 25 times.
Scholar 3.6 years ago, created an answer that has been accepted. For A: warning in R
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