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2021-Emmaneel et al-Cytometry A

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mleipold

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Posts: 5262

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Thu Sep 23, 2021 3:32 pm

2021-Emmaneel et al-Cytometry A

"PeacoQC: Peak-Based Selection of High Quality Cytometry Data"
Annelies Emmaneel, Katrien Quintelier, Dorine Sichien, Paulina Rybakowska, Concepción Marañón, Marta E Alarcón-Riquelme, Gert Van Isterdael, Sofie Van Gassen, Yvan Saeys
Cytometry A. 2021
https://doi.org/10.1002/cyto.a.24501

"Four different datasets were used for the generation of the results where PeacoQC is compared to three other algorithms. The first dataset is an inhouse dataset where three different types of anomalies were deliberately introduced during measurements on the flow cytometer using four mice spleen samples. The second dataset consists of one mass cytometry fcs file measured on human whole blood while the third dataset consists of a spectral cytometry file measured on mouse spleen. The mass cytometry file was provided by the GENYO institute. [...] The first three datasets are available at flowRepository ID FR-FCM-Z3YQ together with the svg files of the fourth dataset and an overview of which of the FlowCAP IV files were used. The FlowCAP IV files themselves can be accessed through flowRepository ID FR-FCM-ZZ99.

FR-FCM-Z3YQ: "Sorry, you do not have access to the specified experiment"

"Additionally, we wanted to ensure that the default PeacoQC parameter choices are suitable for a wide range of datasets. To evaluate this, we selected all samples on flowRepository which fit the following criteria: the datasets had to be uploaded or updated in 2020, the data had to be published in Cytometry Part A and could not include data of other datasets, only samples that contained cells and were fully stained were selected and the samples could not be altered during their measurement since we expect a stable signal over time. The information of the selected datasets can be found back in Supplementary Table 1. In total we analysed 9 flow cytometry datasets, 3 mass cytometry datasets and 4 spectral cytometry datasets."

3 mass cytometry datasets:
FR-FCM-Z2NR: 2020-Rybakowska et al-Cytometry A
FR-FCM-Z2NX: 2020-Rybakowska et al-Cytometry A
FR-FCM-Z23C: 2020-Rein et al-Cytometry A
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mleipold

Guru

Posts: 5262

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Wed Sep 28, 2022 7:29 pm

Re: 2021-Emmaneel et al-Cytometry A

FR-FCM-Z3YQ now accessible
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Ezequiel

Participant

Posts: 5

Joined: Tue Feb 09, 2021 8:33 pm

Post Tue Dec 20, 2022 1:39 pm

Re: 2021-Emmaneel et al-Cytometry A

This package seems to perform very well on my Mass Cytometry data. Unfortunately there is something off when reloading the cleaned files to Flowjo, where all the events are out of the Time scale. I wonder whether somebody experienced something similar. Thanks a lot!
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tomash

Contributor

Posts: 24

Joined: Sun Oct 19, 2014 10:15 pm

Post Wed Dec 21, 2022 2:59 am

Re: 2021-Emmaneel et al-Cytometry A

Try submitting an issue on the PeacoQC Github page: https://github.com/saeyslab/PeacoQC/issues.

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