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Bishop-Laboratory / correlationAnalyzeR-ShinyApp

A web application interface for correlationAnalyzeR
https://gccri.bishop-lab.uthscsa.edu/shiny/correlation-analyzer/
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Results on CorrelationAnalyzer site and R script results differ #5

Open yotamroshuji opened 4 weeks ago

yotamroshuji commented 4 weeks ago

Hi, Using the site and the DB I get different for Pearson Correlation. For example, the gene GOT1 shows completely different results. Which source is the correct one for Pearson Correlation results? Thanks!

millerh1 commented 3 weeks ago

@yotamroshuji Could you provide additional details? Please include the commands you are using to get these results from the DB and share the results you got from the DB and the website.

yotamroshuji commented 3 weeks ago

When searching for "GOT1" on the CorrelationAnalyzeR site, the results are the same forSample Type = Cancer and All. In the R package I get different results:

analyzeOutputCancer <- analyzeSingleGenes(
  "GOT1",  Tissue = "all", Sample_Type = "cancer",
  runGSEA = FALSE
)
analyzeOutputAll <- analyzeSingleGenes(
  "GOT1",  Tissue = "all", Sample_Type = "all",
  runGSEA = FALSE
)
analyzeOutputCancer$correlations["GOT2",]  # Results in 0.73
analyzeOutputAll$correlations["GOT2",]     # Results in 0.766

By the way, is the data on the site updated for today's ARCHS4 data? It has been a really great source for expression data.