search

ThomasMZheng / Proteomics-BQC

All of the work done while a part of the Richards Lab will be here
0 stars 0 forks source link

2023/10/23 #3

Closed ThomasMZheng closed 11 months ago

ThomasMZheng commented 11 months ago

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

ThomasMZheng commented 11 months 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.