Question: how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data?
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gravatar for lhaiyan3
11 months ago by
lhaiyan320
United States
lhaiyan320 wrote:

Dear all:

Did anyone use ESTIMATE (http://bioinformatics.mdanderson.org/main/ESTIMATE:Overview) to infer tumor purity and stromal score from RNA-seq before? I am not clear how to use this tool and what is the input file format for this tool? They are just several steps, and i did not figure out how to load my own data to run the program? Thanks very much for your great help.

OvarianCancerExpr <- system.file("extdata", "sample_input.txt", package="estimate") filterCommonGenes(input.f=OvarianCancerExpr, output.f="OV_10412genes.gct", id="GeneSymbol") estimateScore("OV_10412genes.gct", "OV_estimate_score.gct", platform="affymetrix") plotPurity(scores="OV_estimate_score.gct", samples="s516", platform="affymetrix")

best

Haiyan Lei

rna-seq • 953 views
ADD COMMENTlink modified 6 months ago by sina.nassiri20 • written 11 months ago by lhaiyan320
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gravatar for sina.nassiri
6 months ago by
sina.nassiri20
Switzerland/Lausanne
sina.nassiri20 wrote:

The ESTIMATE algorithm (Yoshihara et al. 2013 Nature Communications) is comprised of two steps. In the first step, an enrichment score is calculated using single-sample GSEA (Barbie et al. 2009 Nature). Note that although immune cells are essentially part of the stroma, Yoshihara et al. calculated two enrichment scores. One based on immune-related genes, which they referred to as "immune" score. The other score was calculated based on non-immune genes, which they referred to as "stromal" score. The final ESTIMATE score is the sum of immune and stromal enrichment scores. In the second step, the ESTIMATE enrichment score is converted to tumor purity using the following formula:

Tumour purity = cos (0.6049872018 + 0.0001467884 􏰀 x ESTIMATE score)

where "Tumor purity" represents ABSOLUTE-based tumor purity (ABSOLUTE is another algorithm that computes tumor purity based on somatic DNA copy number alterations), and "ESTIMATE score" represents ESTIMATE enrichment score obtained from TCGA Affymetrix data, as explained above. The key point is that this calibration formula was derived using only Affymetrix data, and therefore cannot be used to convert RNAseq-based ESTIMATE score to tumor purity. That being said, you may still apply the single-sample GSEA algorithm to properly normalized RNAseq data to obtain ESTIMATE enrichment scores, and incorporate them as covariate in your downstream analysis to account for tumor purity.

ADD COMMENTlink modified 6 months ago • written 6 months ago by sina.nassiri20

This does not answer the question.

ADD REPLYlink written 4 months ago by friendshipweekpoem0

"The key point is that this calibration formula was derived using only Affymetrix data, and therefore cannot be used to convert RNAseq-based ESTIMATE score to tumor purity" ... How does this not answer the question?

ADD REPLYlink written 3 months ago by sina.nassiri20
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