User: kakukeshi

gravatar for kakukeshi
kakukeshi50
Reputation:
50
Status:
Trusted
Location:
Last seen:
1 month ago
Joined:
2 years, 9 months ago
Email:
k********@gmail.com

Posts by kakukeshi

<prev • 36 results • page 1 of 4 • next >
0
votes
2
answers
93
views
2
answers
Answer: A: Add gene name in ComplexHeatmap
... add the argument `row_labels = my_data$Gene` in the function Heatmap. ...
written 5 weeks ago by kakukeshi50 • updated 5 weeks ago by genomax83k
0
votes
0
answers
72
views
0
answers
Pathways enriched across multiple transcriptomics datasets?
... Hi, I did KEGG pathway GSEA of 10 different gene expression datasets (5 of disease 1 and 5 of disease 2). Now, I would like to know if there are pathways enriched in opposite directions in disease 1 versus disease 2 (for example up-regulated across datasets of disease 1 and down-regulated across ...
gene R rna-seq gsea written 5 weeks ago by kakukeshi50
0
votes
1
answer
610
views
1
answers
Comment: C: How to normalize GTEX gene counts with DESeq2?
... oops! its corrected now ...
written 14 months ago by kakukeshi50
3
votes
1
answer
610
views
1
answer
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 14 months ago by kakukeshi50 • updated 13 months ago by Biostar ♦♦ 20
0
votes
1
answer
922
views
1
answers
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 14 months ago by kakukeshi50
0
votes
1
answer
922
views
1
answers
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 14 months ago by kakukeshi50
0
votes
1
answer
922
views
1
answers
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 14 months ago by kakukeshi50
2
votes
1
answer
922
views
1
answer
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 14 months ago by kakukeshi50 • updated 14 months ago by Kevin Blighe59k
0
votes
1
answer
409
views
1
answer
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 15 months ago by kakukeshi50 • updated 15 months ago by EagleEye6.6k
0
votes
0
answers
599
views
0
answers
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 21 months ago by kakukeshi50

Latest awards to kakukeshi

Popular Question 7 months ago, created a question with more than 1,000 views. For Parse Drugbank XML in R
Popular Question 12 months ago, created a question with more than 1,000 views. For Parse Drugbank XML in R
Popular Question 21 months ago, created a question with more than 1,000 views. For Parse Drugbank XML in R

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 806 users visited in the last hour