2022-Khan et al-preprint
"Complicated Common Variable Immunodeficiency is Driven by Aberrant IL-10/IL-21 Signaling and Predisposed Polygenic Risk"
Humza A Khan, Utkucan Acar, Alexis V Stephens, Timothy J Thauland, Manish J Butte
medRxiv, posted June 21, 2022
https://doi.org/10.1101/2022.06.20.22276681
- will update when/if this is peer-reviewed and published
- "Data Availability All data produced in the present work are contained in the manuscript, hosted at https://github.com/humzalikhan/CVID_CyTOF_PRS, or otherwise are available upon request."
- I don't see any FCS files here; there are some R objects, but that's it as far as I can tell.
- I'm also a bit puzzled by this comment about the zeroes in the data:
"Batch Effect Correction
Phosphorylation values from different experimental dates were adjusted to allow for accurate comparisons despite batch effects. The unstimulated Gaussian mixture model phosphorylation values from a date’s control were used to adjust each cell type-signaling pathway combination for all stimuli as was previously described(16). Values of zero were removed from the data and are common statistical noise in all CyTOF datasets. "
Humza A Khan, Utkucan Acar, Alexis V Stephens, Timothy J Thauland, Manish J Butte
medRxiv, posted June 21, 2022
https://doi.org/10.1101/2022.06.20.22276681
- will update when/if this is peer-reviewed and published
- "Data Availability All data produced in the present work are contained in the manuscript, hosted at https://github.com/humzalikhan/CVID_CyTOF_PRS, or otherwise are available upon request."
- I don't see any FCS files here; there are some R objects, but that's it as far as I can tell.
- I'm also a bit puzzled by this comment about the zeroes in the data:
"Batch Effect Correction
Phosphorylation values from different experimental dates were adjusted to allow for accurate comparisons despite batch effects. The unstimulated Gaussian mixture model phosphorylation values from a date’s control were used to adjust each cell type-signaling pathway combination for all stimuli as was previously described(16). Values of zero were removed from the data and are common statistical noise in all CyTOF datasets. "