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2022-Khan et al-preprint

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mleipold

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Posts: 3745

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Wed Jun 22, 2022 9:28 pm

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. "
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sgranjeaud

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Posts: 111

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Wed Jun 22, 2022 9:56 pm

Re: 2022-Khan et al-preprint

In the text of the preprint, only Code Availability is stated. The data availability on medRxiv sounds like a copy of this statement.
Concerning the batch correction, I hope to find more details in Choi et al.
The removal of zeroes nor "common statistical noise" are neither argued nor sourced.

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