Christophe Vanderaa

@TTCooper_PhD @SCP_meeting Same here

@SCP_meeting Is this correct? I am trying the zoom link I was sent on Friday.

Our 7th meeting has began ! single-cell.net/proteomics/scp…

@rah_ds @slavovLab Sorry for the late reply, but yes we are treating the cells as independent. I am currently working on extending the framework to include correlation structure caused by biological or technical replication, so stay tune😁

@c_vanderaa @slavovLab great stuff! But are you treating the single-cells as independent? From the plot it looks like it.

Our new preprint is available on biorXiv: doi.org/10.1101/2023.1… !🥳 We present scplainer, a principled computational approach to streamline and standardise #MassSpec #SingleCell #proteomics data analysis. Here's a 🧵 with our key messages.

@lgamon Interesting question! I see no reason why scplainer would not work on spatial low-sample data, although I did not try it (yet?). An obvious limitation I see is that scplainer cannot take advantage of the spatial information. Suggestions for extensions of the method are welcome😉

@c_vanderaa Including spatial low sample (non-single cell) data? Eg 4x4 arrays from different tissue microregions?

As always, many thanks to my promoter Laurent Gatto for his supervision. I also warmly thank Manon Martin and Bernadette Govaerts for their guidance on the APCA+ framework.

scplainer will be (very) soon available in scp so that you can try it yourself. Need data? All data used in this work were retrieved using our scpdata package! github.com/UCLouvain-CBIO… github.com/UCLouvain-CBIO…