Hi everyone,

Currently, I'm analyzing a RNA-seq quantification method RNA-SKIM. Since I'm completely new in this area, let me explain my problem with an example.

As you can see from the link, in figure 8 RNA-skim validates its result on a real dataset by comparing it with other algorithms that do the same thing. In order to do that they use Pearson Correlation Vs Spearman Correlation chart.

My question is that, each of the black dots on the chart represents the result of RNA-skim on a different dataset or does all of the black points together represents the single dataset result.

Result of RNA-SKIM consist of 5 columns and they are:

transcript ID      length of transcript     estimated number of reads     RPKM value  TPM value of transcript

So, to make my first question more clear, does the black point represent a single line of this result file or each point represents such a txt file? I think each of the dots are corresponds to a complete file but I am not sure about that.