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mcanouil / NACHO

NAnostring quality Control dasHbOard
https://m.canouil.dev/NACHO/
GNU General Public License v3.0
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Pos and neg controls in RCC file #32

Closed ChadAHighfill closed 2 years ago

ChadAHighfill commented 2 years ago

Please include a minimal reproducible example (AKA a reprex). If you've never heard of a reprex before, start by reading https://www.tidyverse.org/help/#reprex.

Hey Nacho team, when reading in my RCC files, each one harbors the internal positive and negative controls, labeled POS and NEG. How does this affect the predict housekeeping genes?

# insert reprex here
mcanouil commented 2 years ago

POS/NEG are used to normalise the data at a more technical level. This includes housekeeping genes.

Housekeeping genes are used (when available through NanoString panel or "prediction") to normalise the data at a "biological level".

ChadAHighfill commented 2 years ago

Hi Mcanouil, this means, that the POS/NEG labels would not influence the predicted housekeeping genes?

mcanouil commented 2 years ago

POS/NEG are technical controls with known concentrations of biological materials, thus has nothing to do with your biological samples and/or housekeeping genes. Their sole purpose is to be used to correct technical bias that might arise.