ThomasMZheng
commented
1 year ago SS-200150_v4_ACDPlasma.hybNorm.medNormInt.plateScale.calibrate.anmlQC.qcCheck.medNormRefSMP.adat can also be found in /project/richards/restricted/BQC19_Releases/V6/Datasets/Somalogic along with SS-215174.hybNorm.medNormInt.plateScale.medNormRefSMP.anon.adat
As such, first I need to figure out if there is any overlap between the two datasets.
They look like two completely different samples, will need to figure out how to merge the datasets - Chen-Yang wrote about this on his github.
From the hydra cluster, BQC19-Somalogic data was downloaded/loaded onto the R server.
Documentation
There were four files availalbe from /project/richards/restricted/BQC19_JGH/Data_sources/Genetics_Metabolomics_Proteomics/Proteomics/20201120
These files were: MCG-200150.zip SomaDataIO_3_1_0_and_pdf.zip McGill-Richards-C-19-SomaScan-Data.zip 'SSM-00060 - Rev 1.0 - Data Standardization and File Specification Technical Note.pdf'
However, "McGill-Richards-C-19-SomaScan-Data.zip" is just a zipped folder containing the MCG-200150.zip, SomaDataIO...zip, and the "SSM" pdf.
The SomaDataIO.zip is a R package that allows for the analysis of SomaScan's .adat files
So the only relevant files/folders present are the "SSM-00060 - Rev 1.0 - Data Standardization and File Specification Technical Note.pdf" and the "MCG-200150.zip".
MCG-200150.zip
The MCG zip contains a pdf, an xlsx, and two .adat files. The pdf is a SomaScan Quality Statement (SQS), the xlsx is more QC, and the two .adat files are :
Normalized data reported: SS-200150_v4_ACDPlasma.hybNorm.medNormInt.plateScale.calibrate.anmlQC.qcCheck.medNormRefSMP.adat
Data are also reported without sample normalization applied for analysts to evaluate alternate normalization methods. SS-200150_v4_ACDPlasma.hybNorm.medNormInt.plateScale.calibrate.anmlQC.qcCheck.adat