Incompatibility with Updated LabWorksheet Format from GeoMx DSP Control Center v3.1.0.222

[EmanuelSoda]

Hello GeomxTools Team,

First of all, thank you for developing and maintaining this excellent package and platform. It has been incredibly useful for my work.

I have encountered an issue with the readNanoStringGeoMxSet() function related to the LabWorksheet file obtained from the GeoMx DSP Control Center (v3.1.0.222). Previously, the LabWorksheet was available as an Excel file, which worked seamlessly with the readNanoStringGeoMxSet() function by specifying the SampleAnnotationFile (i.e., the LabWorksheet) and the phenoDataSheet within the Excel file.

However, it appears that the LabWorksheet is no longer provided in Excel format in the latest version of the GeoMx DSP Control Center. As a result, the readNanoStringGeoMxSet() function is unable to process the LabWorksheet, leading to errors.

I was wondering if:
1. Is this issue specific to my setup, or is it due to an incompatibility introduced by the recent update in the GeoMx DSP Control Center?
2. If it’s an incompatibility, could you please provide an update or guidance on how to adapt GeomxTools to accommodate the new format of the LabWorksheet?

Could you please investigate this issue and consider providing an update to GeomxTools that supports the new LabWorksheet format? Additionally, if this issue has already been resolved in a newer version, guidance on updating would be greatly appreciated. Any assistance or workaround you can provide would be immensely helpful.

Thank you for your time and support!
Best regards,
Emanuel Soda

Additional Information:
• GeoMx DSP Control Center Version: 3.1.0.222
• GeomxTools Version: 3.6.2 Bioconductor version
• R Version: 4.3.1

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