User: thyagoleal

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thyagoleal30
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Posts by thyagoleal

<prev • 13 results • page 1 of 2 • next >
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Comment: C: limma-voom duplicateCorrelation once or twice, difference?
... Thanks, Gordon. Sure, I'll use treat() for that. ...
written 14 days ago by thyagoleal30
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Comment: C: limma-voom duplicateCorrelation once or twice, difference?
... Thank you, Aaron. ...
written 14 days ago by thyagoleal30
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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 15 days ago by thyagoleal30 • updated 14 days ago by Gordon Smyth35k
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Comment: C: RankProd crashing - stability issues?
... Hi, I'm having the same issue. Did you find a solution? Thanks ...
written 11 months ago by thyagoleal30
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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 14 months ago by thyagoleal30
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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 14 months ago by thyagoleal30
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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 15 months ago by thyagoleal30
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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 15 months ago by thyagoleal30 • updated 15 months ago by Wolfgang Huber13k
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Answer: A: biomaRt Ensembl ID query returns NA in 'ensembl_gene_id', 'ensembl_transcript_id
... Have you checked if the input ids are correct? I mean, are you telling what they're correctly? If so, try using another annotation. ...
written 16 months ago by thyagoleal30
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Answer: A: RSQLite reverse dependencies
... Are you using R in which operating system? If linux, you may have to install some dependencies via terminal, such as RSQLite.     ...
written 16 months ago by thyagoleal30

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