User: ivykosater

gravatar for ivykosater
ivykosater0
Reputation:
0
Status:
New User
Last seen:
8 hours ago
Joined:
1 month, 1 week ago
Email:
i*********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by ivykosater

<prev • 6 results • page 1 of 1 • next >
0
votes
0
answers
102
views
0
answers
Using TCGABioLinks to query multiple cancer studies
... I have a list of cancer samples that I wish to download transcriptome data for using TCGABiolinks. I use the GDCquery() function for downloading data, however my list spans multiple TCGA projects. Here is my code query <- GDCquery(project = "", data.category = "Transcriptome Profiling", ...
R tcga rna-seq written 4 weeks ago by ivykosater0
0
votes
0
answers
128
views
0
answers
Comment: C: GSVA Error: "Less than two genes in the input expression data matrix"
... No particular reason. Here are the first few rows and columns of expr expr Name Description TCGA-C8-A1HM-01 TCGA-D8-A1XQ-01 4 "LINC02082" "ENSG00000242268.2" "0.0" "0.0" ...
written 5 weeks ago by ivykosater0
0
votes
0
answers
128
views
0
answers
GSVA Error: "Less than two genes in the input expression data matrix"
... I have a matrix of gene expression data for multiple samples from TCGA which I converted into a matrix from a GCT file. # Convert to R dataype expr <- read.csv("BRCA_dataset2.gct", sep = "\t", header=FALSE) # Clean up the data expr <- expr[-2,] expr <- expr[-1,] ...
R gsva rna-seq gsea written 5 weeks ago by ivykosater0
0
votes
1
answer
104
views
1
answers
Comment: C: Creating a cls file from two groups of TCGA RNA-seq samples
... Hi Kevin, thanks for the summary. Was curious if you knew a way I could assign a phenotype label that corresponds to the each sample. I have a list of samples with the mutation and without, but going through 3000 samples assigning labels to each seems tedious. Perhaps I could use an R script. ...
written 5 weeks ago by ivykosater0
0
votes
1
answer
104
views
1
answer
Creating a cls file from two groups of TCGA RNA-seq samples
... I want to look at two separate groups of TCGA-BRCA RNA-seq samples. One with a specific mutation and one without. What I have done is download the RNA-seq expression for all the TCGA-BRCA samples and create a gct file. However, I am unsure of how to create a cls file which designates the samples as ...
R tcga rna-seq gsea written 5 weeks ago by ivykosater0 • updated 5 weeks ago by Kevin Blighe71k
0
votes
0
answers
107
views
0
answers
TCGABioLinks getManifest() function. How to alter saved file name?
... In the TCGABioLinks R package there is a function called `getManifest()` which allows you to download queries samples manifest files. I have two datasets that I'm trying to pull. One is a set of tumor samples with a specific mutation, the other is the set of samples without said mutation. What I'v ...
R bioconductor tcga written 5 weeks ago by ivykosater0

Latest awards to ivykosater

Autobiographer 5 weeks ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 968 users visited in the last hour
_