Normal vs Tumor - Kaplan Meier Survival Analysis
0
0
Entering edit mode
4 months ago
Gnana • 0

To perform survival analysis for normal vs tumor cancer sample what kind of rna seq data is to used?

  • unstranded
  • stranded_first
  • stranded_second
  • tpm_unstrand
  • fpkm_unstrand
  • fpkm_uq_unstrand

Which of these shoud be used and is there any normalisation to be done?

fpkm Survival-Analysis rpkm • 556 views
ADD COMMENT
2
Entering edit mode

Survival analysis tumor vs normal? I can already tell you that normal survives longer than tumor. Please add some details what exactly you want to do because the question as by now makes no sense.

ADD REPLY
0
Entering edit mode

I want to check the survival for a specific gene in normal vs tumor condition in Tcga data.

ADD REPLY
0
Entering edit mode

What do you mean by "survival of a gene"?

ADD REPLY
0
Entering edit mode

Your first question - use GDCquery - it takes care of loading the expression data:

mrna_query <- GDCquery(project = "TCGA-PRAD",
                       data.category = "Transcriptome Profiling",
                       data.type = "Gene Expression Quantification",
                       workflow.type = "STAR - Counts",
                       experimental.strategy = "RNA-Seq")

GDCdownload(mrna_query, method = "api", files.per.chunk = 100,
            directory = "~/Desktop/TCGA/mRNA/")

mrna_df <- GDCprepare(mrna_query, directory = "~/Desktop/TCGA/mRNA/")

Yes normalisation is required:

y <- edgeR::DGEList(mrna_df)
y <- edgeR::calcNormFactors(y)
logcpm <- edgeR::cpm(y, normalized.lib.sizes = T, log=TRUE)

Follow up on ATpoints comment because he is 100% correct:

Take a look at GEPIA: http://gepia.cancer-pku.cn/index.html to look at survival plots for a single gene in a TCGA dataset

In GEPIA, the two lines in the kaplan-meier plot represent patients stratified into two groups using median gene expression cutoff... each group containing normal and tumor samples...

ADD REPLY

Login before adding your answer.

Traffic: 2922 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6