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Erica Pawlak, one of our awesome Field Applications Scientists, wants you to know how to set up pairwise ratios in nSolver.

It is common, particularly in clinical and translational research, to design experiments that allow each experimental measurement to be compared back to its own, matched, control.  Examples of this would include: comparing tumor samples to healthy tissue samples (from the same individual), or comparing samples taken before treatment to samples taken after treatment.  Letting each individual serve as its own control reduces the impact of variance between individuals across your experiment population.

Statistically, the appropriate test for this experimental design is the Paired T-test.  This version of the t-test will determine if the mean difference between the paired measurements is significantly different from the null hypothesis, or zero.  While basic nSolver does not make paired comparisons, it is possible to set up this comparison using the Advanced Analysis module.  By creating two variables for each sample, one identifying the individual, and the other identifying a second variable (such as treatment), we are able to set Advanced Analysis up to subtract any individual-to-individual variation from the overall change in expression.

ratio 1For example: Let’s say you have multiple patient samples (A,B,C…F) and they have all undergone the same treatment.  You’ve tested them pre-treatment and then again post-treatment and you’d like to do a paired comparison for each sample between their pre- and post-treatment results.

Here’s how to set this analysis up in nSolver:

  1. In the Sample Annotation step of creating an experiment, click Create Annotation twice, creating two columns.
  2. Define one column Sample Name and the other, Treatment.
  3. Fill the annotations in each column for the samples, A-F for Sample Name and pre or post for Treatment.
  4. In the Build Ratios step, select Partitioning by and choose Treatment and pre from the drop-down boxes.blog 3

Voilà! nSolver will generate all pairwise ratios for each sample pair.



FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.

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Posted by Joe Horsman