User: aaragak1

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aaragak140
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Posts by aaragak1

<prev • 15 results • page 1 of 2 • next >
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Repository for Individual Patient Data
... I'm doing some research into immunotherapies and patient outcomes, but I also want to do some work with the associated gene expression data - thus requiring that I have matched genetic and clinical data. I'd additionally prefer to work with publicly available datasets. Is there some easy way for m ...
data collection written 3 months ago by aaragak140
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Comment: C: Graph 1 gene against a group of gene
... Hello! Hope you're doing well. Have you tried using something like GSVA? That is able to give you an enrichment score per-sample for a given geneset or multitude of genesets ...
written 7 months ago by aaragak140
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Comment: C: R : Plotting several variables using ggplot geombar
... Off the top of my head, you might be able to use `dplyr`s `mutate` + `case_when`, or perhaps an `as.factor`? I'm not entirely sure what the current levels of the column is right now ...
written 7 months ago by aaragak140
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Answer: A: R : Plotting several variables using ggplot geombar
... I've tried something like this - let me know if this is what you were going for library(tidyverse) set.seed(1) reprex <- tibble(sample = rep(c("HSV", "MOCK", "VRS"), each = 300), proto = rep(c("E", "M", "Q"), each = 100, times = 3), ...
written 7 months ago by aaragak140
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Comment: C: R : Plotting several variables using ggplot geombar
... Hello! I hope you're keeping well. What happens when you use `sampledupli` as your faceting variable? I'm trying to generate a toy dataset that I can work with to help you with this problem, but I'm having trouble figuring out what `prop` is referring to exactly. Am I correct in assuming that it ...
written 7 months ago by aaragak140
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Is this a normal mean/variance scRNA plot?
... I've been following bioconductor's OSCA book for some scRNAseq analysis (smart seq2 protocol, no spike-in). After QC, normalization (deconvolution) and transformation (log2, pseudocount 1) upon plotting the mean/variance of the genes, I noticed that the plot looked very much like a negative parabola ...
R rna-seq written 7 months ago by aaragak140 • updated 5 months ago by Biostar ♦♦ 20
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Comment: C: GSVA score and 1-Pearson correlation results do not harmonize
... I'm clustering using the normalized, log transformed expression of the 8 or so genes that were used to generate the GSVA score - returning to the roots of the dataset, if you will. I think you bring up a good point about not necessarily seeing two distinct clusters. I think was confused me the most ...
written 7 months ago by aaragak140
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Comment: C: GSVA score and 1-Pearson correlation results do not harmonize
... Histogram of enrichment scores, showing bimodality: ![Histogram of Enrichment Scores][1] Hierarchical clustering using a euclid distance metric ![Hierarchical Clustering, Euclid Distance][2] Hierarchical clustering using a 1- pearson correlation distance ![Hierarchical Clustering, Pearson Di ...
written 7 months ago by aaragak140
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Comment: A: Ensembl ID to ENTREZ best converter
... BioMart, as others have mentioned, tends to work pretty well. Have you removed the version numbers off the end of the ensembl ID? (ie 1234567.89 --> 1234567) ...
written 7 months ago by aaragak140
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GSVA score and 1-Pearson correlation results do not harmonize
... I calculated `GSVA` scores for a large set of tumors using a fairly small set of genes (~8 genes in the signature). I found there to be a distinct bimodal distribution in my data (yes, `mx.diff = T`). I then wanted to see if I could 'orthogonally' verify this by hierarchical clustering the tumors ...
R gsva clustering written 7 months ago by aaragak140

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Scholar 7 months ago, created an answer that has been accepted. For A: R : Plotting several variables using ggplot geombar

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