User: Pietro

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Pietro60
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Posts by Pietro

<prev • 22 results • page 1 of 3 • next >
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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 26 days ago by Pietro60
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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 26 days ago by Pietro60
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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 26 days ago by Pietro60 • updated 26 days ago by Kevin Blighe44k
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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 9 weeks ago by Pietro60
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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 9 weeks ago by Pietro60
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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 9 weeks ago by Pietro60
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Fold change cut off enrichment analysis
... I would like to hear your opinion about this approach. I am doing over-representation analysis on differentially expressed genes from RNA-Seq. Instead of doing a single test, let's say, for up-regulated genes with a log2FC cut off of x, I am doing different test within different cut off intervals. ...
enrichment cutoff ontology rna-seq fold change written 9 weeks ago by Pietro60 • updated 9 weeks ago by shawn.w.foley750
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Comment: C: Experimental design RNAseq differential expression
... You mean design <- model.matrix(~ 0 + cellLine + time, levels = samples_table) ? And then I have a b c d e f time48 time168 1 1 0 0 0 0 0 0 0 2 1 0 0 0 0 0 1 0 3 ...
written 3 months ago by Pietro60
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Comment: C: Experimental design RNAseq differential expression
... Hi Devon, Realized that. So, what do you suggest to account for `cellLine` in my design? Thanks ...
written 3 months ago by Pietro60
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Comment: C: Experimental design RNAseq differential expression
... Thanks Kevin, Tried that, but it throws an "Design matrix not of full rank" error. ...
written 3 months ago by Pietro60

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Popular Question 16 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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