User: thyagoleal

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thyagoleal20
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Posts by thyagoleal

<prev • 9 results • page 1 of 1 • next >
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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 3 months ago by thyagoleal20
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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 ...
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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 4 months ago by thyagoleal20
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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 4 months ago by thyagoleal20 • updated 4 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 4 months ago by thyagoleal20
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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 4 months ago by thyagoleal20
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Answer: A: Getting gene annotation for a GEO dataset
... Well, it seems like the file was badly composed, perhaps. I couldn't get a proper Expression Matrix with GEOquery as well.  Maybe can you get in touch with the authors?   ...
written 4 months ago by thyagoleal20
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Plotting Gene Expression Data From Multiple Batches
... I'm currently analyzing 4 microarray experiments in an integrated manner. For this, I'm using limma accounting for the batches through the design matrix: design <- model.matrix(~0+Class+Batch, data = phenot) Since removing the batch effects, for example, with Combat is not advisable before DEG ...
microarray plot batch effect written 4 months ago by thyagoleal20 • updated 4 months ago by Jenny Drnevich1.9k
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How can I visualize Gene Set Enrichment Results from gseGo fun. (clusterProfiler)?
... Hi, everyone. I've been using the amazing package clusterProfiler and I have a question about visualizing the results.  Well, I've been using the enrichGo() function and plotting its results (enrichResult obj.) with barplot() and dotplot() functions. Now, I'm using gseGo (another test, similar but ...
visualization clusterprofiler ggplot2 gsego written 7 months ago by thyagoleal20 • updated 7 months ago by Guangchuang Yu800

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