## User: ravelarvargas

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#### Posts by ravelarvargas

<prev • 9 results • page 1 of 1 • next >
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... 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 ...
written 11 weeks ago by ravelarvargas0
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... 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 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 ...
written 6 months ago by ravelarvargas0
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... 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’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 ...
written 6 months ago by ravelarvargas0
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... 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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... 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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... 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 ...
written 7 months ago by ravelarvargas0 • updated 7 months ago by Aaron Lun24k
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... 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 ...
written 12 months ago by ravelarvargas0 • updated 12 months ago by James W. MacDonald51k

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