User: kakukeshi

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kakukeshi50
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Posts by kakukeshi

<prev • 32 results • page 1 of 4 • next >
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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 8 days 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 9 days 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 9 days 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 9 days ago by kakukeshi50 • updated 9 days ago by Kevin Blighe39k
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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 weeks ago by kakukeshi50 • updated 4 weeks ago by EagleEye6.2k
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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 6 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 6 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 6 months ago by kakukeshi50
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Comment: C: Extract specific variants from binary plink files
... check in the log if its really reading the variants in the snps.txt file ...
written 8 months ago by kakukeshi50
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Comment: C: Extract specific variants from binary plink files
... Check using `grep` in the bim file (chr19) grep "rs7412" mydata.bim ...
written 8 months ago by kakukeshi50 • updated 8 months ago by zx87546.8k

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Popular Question 7 months ago, created a question with more than 1,000 views. For Parse Drugbank XML in R

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