User: ravelarvargas

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Posts by ravelarvargas

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(Closed) Manually adding corrected p-values to boxplots in R
... I am using R to add some p-values to boxplots. I would like to specifically compare pairs of boxplots using a wilcoxon rank sum test. I tried using the function stat_compare_means() from ggpubr but unfortunately there is no option to add adjusted p-values. I searched online for a bit and noticed a f ...
R ggplot2 boxplot rstatix ggpubr written 11 weeks ago by ravelarvargas0
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Comment: C: I am having trouble recreating the linear regression results published in an Alz
... I've added a fully reproducible version here https://support.bioconductor.org/p/118615/. Still no luck with the original question unfortunately ...
written 6 months ago by ravelarvargas0
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I am trying to recreate results from an Alzheimer's paper but I can't figure out my linear regression model
... I am trying to recreate the differential gene expression results from the following paper between Alzheimer’s and normal brain donors (https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0355-3). Specifically, the authors divided the brains up into 19 different regions, and divided ...
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Comment: C: I am having trouble recreating the linear regression results published in an Alz
... 1) I contacted four of the authors but unfortunately they all directed me to one of the four authors I contacted who hasn't gotten back to me over a few weeks now. I don't know if he is on holiday or busy but I am at a standstill until I can figure out how they got their results. 2) I got the data ...
written 6 months ago by ravelarvargas0
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I am having trouble recreating the linear regression results published in an Alzheimer's paper
... I’m trying to recreate the results from this Alzheimer’s paper for further analysis (https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0355-3) Specifically, the supplementary table 4A reports genes significantly differentially expressed between brain donors that have Alzheimer’s ...
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Comment: C: My linear regression model is giving me too many differentially expressed genes
... I've just given a subset of the data, it's actually 149 patients, I partitioned just 20 patients because I wanted a small example to post on bioconductor. In terms of why I think there should be DE genes it's because this RNA-seq data is a followup to a previous publication of microarray data for th ...
written 7 months ago by ravelarvargas0
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Comment: C: My linear regression model is giving me too many differentially expressed genes
... thanks for the suggestion! I've tried the following: ``` fit2 <- contrasts.fit(fit, contrast=contr.matrix) fit2 <- eBayes(fit2) # compute p-values topTable(fit2, number = nrow(fit2)) ``` Unfortunately this leads my data to having no significant differentially expressed genes, which I don't th ...
written 7 months ago by ravelarvargas0
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My linear regression model is giving me too many differentially expressed genes
... I am trying to find differential gene expression between diseased and normal individuals. I have multiple factors I need to correct for, including sex, race, and age, but once I correct for them, over 90% of my genes are significantly differentially expressed, even after FDR correction. I am sure I ...
limma edger differential gene expression rna-seq linear regression written 7 months ago by ravelarvargas0 • updated 7 months ago by Aaron Lun24k
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What to do with microarray probes that catch multiple genes?
... I am currently looking at existing differential gene expression data another lab has uploaded to GEO (GSE48761). I have a few issues I don't know how to deal with: 1. How to salvage gene of interest data when one probe grabs multiple genes? For example, I'm interested on the expression of a gene c ...
microarray probe statistics affymetrix microarrays written 12 months ago by ravelarvargas0 • updated 12 months ago by James W. MacDonald51k

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