User: kakukeshi

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kakukeshi50
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Posts by kakukeshi

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Comment: C: How to normalize GTEX gene counts with DESeq2?
... oops! its corrected now ...
written 3 months ago by kakukeshi50
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How to normalize GTEX gene counts with DESeq2?
... Hi, I want to normalize the gene counts from GTEX using variance stabilizing transformation (VST) but I'm confused about which variables I should include in the "design" when creating DESeqDataSet. For the moment I'm doing the following: dds <- DESeqDataSetFromMatrix(countData = gtex, ...
rna-seq written 3 months ago by kakukeshi50 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: GSVA on RNAseq data (GTEX)
... Just one last thing Kevin. I noticed that after the rlog step the samples are not exactly normally distributed (link below), so I scaled the values using `gtex <- apply(gtex, 2, scale)` but after doing that the results from the gsva are different. My question is: is it really meaningful to scale ...
written 4 months ago by kakukeshi50
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Comment: C: GSVA on RNAseq data (GTEX)
... Ups! Thanks Kevin. May I ask you if I should apply some type of filtering for the samples (individuals)? ...
written 4 months ago by kakukeshi50
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Comment: C: GSVA on RNAseq data (GTEX)
... Hey Kevin, This is very helpful. Many thanks. Following your suggestions what I did was to filter genes with low count first from the raw counts file (.gene_reads.gct.gz) using: i.rm <- which(rowSums(subsetdat)<5000) subsetdat <- subsetdat[-i.rm,] Then I transformed the data to ...
written 4 months ago by kakukeshi50
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GSVA on RNAseq data (GTEX)
... I'm using the bioconductor package GSVA (http://bioconductor.org/packages/GSVA) to perform a GSVA analysis using RNA-seq data from GTEX and I'm confused about which dataset I need to use and if I need to perform some pre-processing steps. According to the GSVA package vignette the input should be R ...
R rna-seq written 4 months ago by kakukeshi50 • updated 4 months ago by Kevin Blighe45k
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GO terms from keywords in R
... Hi, I'm looking for a way to retrieve go terms programmatically in R using a set of keywords. Any ideas? Thanks ...
R ontology written 4 months ago by kakukeshi50 • updated 4 months ago by EagleEye6.4k
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Comment: C: Is it possible to combine binary, continuous and ordinal (categorical) data?
... I don't understand what you mean by saying by "come up with a scoring system that best matches a phenotype". Let say you want to do a GWAS of intelligence and you have the results of different exams as quantitative (1 to 10) or ordinal data (very bad, bad, regular, good, excellent). You're saying th ...
written 10 months ago by kakukeshi50
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Comment: C: Is it possible to combine binary, continuous and ordinal (categorical) data?
... Can you give me an example? ...
written 10 months ago by kakukeshi50
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Is it possible to combine binary, continuous and ordinal (categorical) data?
... Hi all, I have different types of data (binary, continuous and ordinal) for 10000 individuals and I would like to combine them into a single variable to do a GWAS. I was thinking to transform everything into a number ranging from 0 to 1 by: Binary: leaving it as it is Continuous: scaling the value ...
R snp gwas written 10 months ago by kakukeshi50

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Popular Question 11 months ago, created a question with more than 1,000 views. For Parse Drugbank XML in R

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