Olink Explore HT Data Walkthrough скачать в хорошем качестве

Olink Explore HT Data Walkthrough

In this video, walk through Psomagen's data delivery file for Olink Explore HT projects. Proteomics Product Manager Lori Mull explains each data field and what to expect. Psomagen is a proud Olink Proteomics Certified Service Provider. Learn more about Explore HT on our website: https://www.psomagen.com/proteomics/o... **** VIDEO TRANSCRIPT **** HT data are delivered in a Parquet file. The Sample ID comes from the sample manifest. The Sample Type indicates whether it's a sample or a type of control. The Well ID and Plate ID are utilized by Psomagen's bioinformatics team when they QC the data to ensure there is no bias. The software automatically assigns a block to each sample in the HT panel. There are eight blocks within the HT panel. These are used for QC purposes. Olink ID refers to the specific library of antibodies that was used to generate this lot of the HT panel. The UniProt ID is the official name for the protein target that's being targeted by this assay. Note that Olink controls do not have UniProt IDs. Assay is typically the gene name. Again, Olink controls won't have that. Assay Type is whether it's a control or whether it's an assay. Panel is only HT, and there are eight blocks within the Olink panel of HT. Counts: these are the raw NGS counts. Note that in all HT datasets, Psomagen provides both the intensity normalized data, as well as the plate control normalized data. The Extended NPX (ExtNPX) is the first and intermediate step in the calculation of normalized protein expression. Intensity normalized protein expression is done by taking the median of that target across all of the plates in the study. Plate control normalization typically begins with the extension controls followed by the median of the IPCs, and then a factor that was empirically determined by Olink at manufacturing that mitigates variability across batches of reagents. Assay QC is done based on internal reference count numbers. Sample QC is also done based on internal reference count numbers. A warning here could indicate some type of interference, possibly with the immunoassay itself. Should you need to contact Olink support for a deeper dive into the data, they may ask you for the software version name, panel archive, or preprocessing software and name. They may even ask which instrument was used to sequence the libraries. As you can see here, this was a NovaSeq X Plus. Intra- and InterCV are only calculated for a subset of assays within the entire panel. Those that have not been utilized get "NaN." All data has been thoroughly QC'd by Psomagen's bioinformatics team before releasing it to any customer. The following information on Sample Block QC Warning, these are based on internal and external controls and really just indicate the potential for some flagging within the data, and advised our team to take a closer look at these values. You would not receive data if there had been an actual problem.