User: tcalvo

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tcalvo30
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5 months, 4 weeks ago
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2 years, 8 months ago
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Posts by tcalvo

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Is it allowed to fit two models to make between and within subjects comparisons
... Thank you, Gordon. There was a mistake in the code for within subject analysis. I fixed it. Ignoring Class differences, is there a problem in doing the within subjects analysis only? To get DEG for treatment stages only? ...
written 10 months ago by tcalvo30
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Is it allowed to fit two models to make between and within subjects comparisons separately?
... Hello, community I have a design initially designed to make comparisons both within (before, during, after treatment) subjects and between subjects (disease, control) possible. However, due to difficulties in obtaining high quality samples, the dataset is now more limiting. **Q: Can I perform wit ...
rnaseq limma edger deseq2 random effects written 10 months ago by tcalvo30
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Comment: C: limma-voom duplicateCorrelation once or twice, difference?
... Thanks, Gordon. Sure, I'll use treat() for that. ...
written 12 months ago by tcalvo30
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Comment: C: limma-voom duplicateCorrelation once or twice, difference?
... Thank you, Aaron. ...
written 12 months ago by tcalvo30
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limma-voom duplicateCorrelation once or twice, difference?
... What is the difference between: A) running voom() + duplicateCorrelation() once or;  B) running voom() + duplicateCorrelation() + voom() + duplicateCorrelation(), twice each? I'm getting more shrunken log2FC (shrunken towards 0) when running case B (see code below). About the experiment I have ...
duplicatecorrelation random effects limma-voom written 12 months ago by tcalvo30 • updated 12 months ago by Gordon Smyth39k
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Comment: C: RankProd crashing - stability issues?
... Hi, I'm having the same issue. Did you find a solution? Thanks ...
written 23 months ago by tcalvo30
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Comment: C: DESEq2 p-values weird distribution under the H0 and fdrtool
... Dear Michael, Added. I confirm not using any lfc cutoff from results() function. I used the default, 0, lfc.  Thank you. ...
written 2.2 years ago by tcalvo30
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DESEq2 p-values weird distribution under the H0 and fdrtool
... I'm analyzing an RNAseq with the following samples/groups:  A = 14 samples, B = 7, C = 7, D = 10 and E = 10. Each sample is independent from another and represents a biological sample from one patient with a different form of a disease X.  I've analysed this experiment with DESEq2 with the "stand ...
rnaseq deseq2 differential gene expression fdrtool written 2.2 years ago by tcalvo30
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Comment: C: Volcanoplot with limma - RAW P-values or Adj.P-Values
... Thanks for your answer. I'm not questioning your decision by making the way you did it, though. I only asked because I wanted to know exactly why, since a lot of people often question me this. Anyway, thank you again. Regards, Thyago ...
written 2.3 years ago by tcalvo30
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Volcanoplot with limma - RAW P-values or Adj.P-Values
... I have noticed that limma's volcanoplot() function uses uncorrected p-values from the MArrayLM objected. My question is: why? I've seen an old post where G. Smyth  mentioned that the FDR-corrected p-values loses some info in comparison to the raw ones. Could someone elucidate this, please? Another ...
limma volcanoplot fdr written 2.3 years ago by tcalvo30 • updated 2.3 years ago by Wolfgang Huber13k

Latest awards to tcalvo

Popular Question 11 months ago, created a question with more than 1,000 views. For How can I visualize Gene Set Enrichment Results from gseGo fun. (clusterProfiler)?
Popular Question 11 months ago, created a question with more than 1,000 views. For Volcanoplot with limma - RAW P-values or Adj.P-Values
Popular Question 12 months ago, created a question with more than 1,000 views. For Volcanoplot with limma - RAW P-values or Adj.P-Values

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