1. R2 Frequently Asked Questions (FAQs)

A collections of questions and answers about the R2 platform

1.1. General questions.

  1. Which platforms does R2- support?
  2. Can I shield my data up to publication?
  3. Which kind of data does R2 support?
  4. Which expression data platforms are supported by R2?
  5. Can I analyse my date within a collaborative setting?
  6. Why can’t I see survival data in my dataset of interest?
  7. Can I upload my own data?
  8. How can I make corrections to data that I already submitted?
  9. How can I delete my own dataset or make my dataset public?
  10. Is there a list of platforms R2 is currently supporting?
  11. If I use the datagrabber I don’t get the sample annotation with it?

1.2. Analysis questions.

  1. A Gene Ontology analyses results in a category of more then 100 entries how can I identify the individual genes?
  2. When I perform a hierarchical clustering how can I cluster for each group separately?
  3. When I perform a K-means clustering how can extract the gene order from the program?
  4. When I use the GEO analysis tool and compare the resulting gene list I get a different gene list (70% overlap) compared to the result of the “Find differential expression” option of R2. Is there an explanation for this descrepancy?
  5. Using the R2 grabber I got different expression levels from the same dataset compared to the TCGA alternative
  6. How do I retrieve a list of differentially expressed genes between two or more datasets
  7. In a certain article the gene name which was linked to a probe identifier gives a different gene name
  8. Why can’t I use every dataset in the megasamples analyses.

1.3. Adapting visuals.

  1. How can I mark a sample
  2. Can I generate a SVG-plot with R2.
  3. Is it posssible to add an trendline in XY plot