User: Pietro

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Pietro90
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Location:
Italy
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2 months, 1 week ago
Joined:
3 years, 12 months ago
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Posts by Pietro

<prev • 26 results • page 1 of 3 • next >
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Comment: C: How to proceed after removing batch effect with limma?
... Be careful because the Likelihood ratio test is just a different test from the default Wald test. The LRT is not something specifically related to the batch effect. From DESeq2 vignette `"The LRT is therefore useful for testing multiple terms at once, for example testing 3 or more levels of a fac ...
written 4 months ago by Pietro90
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Comment: C: Question about gene ontology data visualization
... Then maybe you could draw a network of the pathway with Cytoscape and highlight your genes with colors corresponding to maybe fold change or pvalue from an enrichment test. ...
written 4 months ago by Pietro90
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Answer: A: How to proceed after removing batch effect with limma?
... Dear slapiv, Some RNA-Seq guru might help here, but I think that, including batch in the design formula as you did, is fine and nothing else is required. (from DESeq2 vignette, Quick start section, `~ batch + tissue`). Usually what I do is to remove the batch effect from the normalized matrix for ...
written 4 months ago by Pietro90
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Answer: A: Question about gene ontology data visualization
... There are several ways to visualize the results of a functional annotation. Also depending of the type of analysis performed. With the results of a Gene Ontology enrichment analysis I like a simple and elegant bar plot with -log10 of the adjusted pvalue on the x axis, like this: With other visu ...
written 4 months ago by Pietro90
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Comment: C: z score transformation by population or by gene?
... https://www.biostars.org/p/141589/ Or you mean an article? ...
written 5 months ago by Pietro90
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Comment: C: z score transformation by population or by gene?
... My question was more like: "Is it better to scale by global or by gene mean and SD?" ...
written 5 months ago by Pietro90
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z score transformation by population or by gene?
... In calculating z-scores for microarray or RNA-Seq data, I have found two main answers on how to obtain them. For example, in `R`, having a log2 expression matrix `x` with genes in rows and samples in columns, I would do: zscore <- function(x) { z <- (x - mean(x)) / sd(x) return(z ...
z score microarray rna-seq transformation written 5 months ago by Pietro90 • updated 5 months ago by Kevin Blighe51k
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Comment: C: How to normalize NCI-60 gene expression data
... If data are already standardized, then you should check how the z-scores were calculated. Usually z-scoring means subtracting population mean and then dividing by standard deviation, but for gene expression can also mean subtracting row mean and dividing by row SD. See [here][1]. If you can't fin ...
written 6 months ago by Pietro90
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Comment: C: Fold change cut off enrichment analysis
... Hi Shawn, thanks for your answer. I know what GSEA is but I am not sure it can answer my questions for this particular hypothesis. My question was more like "Do genes that are significantly up regulated within a specific FC interval show enrichment for some categories/ontologies/terms, compared to ...
written 6 months ago by Pietro90
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Answer: A: What is the best way to rank genes for GSEA?
... Hi Gabriel For GSEA, some they do `signed fold change * -log10pvalue`, found it here: http://crazyhottommy.blogspot.com/2016/08/gene-set-enrichment-analysis-gsea.html ...
written 6 months ago by Pietro90

Latest awards to Pietro

Appreciated 3 months ago, created a post with more than 5 votes. For A: What is the best way to rank genes for GSEA?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What is the best way to rank genes for GSEA?
Popular Question 21 months ago, created a question with more than 1,000 views. For How to check if a gene is comprised in a certain interval? with R

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