April 30, 2014  |  Announcements  |  By  |  0 Comments

FCS File Quality Control Validation

With the recent rise in cytometry data post-processing (e.g., normalization, debarcoding, concatenation), we at Cytobank have seen many FCS files that do not conform to the ISAC specification, and some of these variations in file writing may lead to downstream errors. As a result, we’ve implemented a Quality Control validator, built into Cytobank, that determines the compliance of your FCS files compared with the specification.

What does it mean for an FCS file to be written to specification? The International Society for Advancement of Cytometry (ISAC) has long-standing specifications that detail the way in which FCS file-writing software should standardize how files are written. This includes information in the file header such as keywords, information about the number of events contained in the files, etc. Analysis platforms rely on this framework to conform to the industry standard in order to guarantee integrity of analysis output. What is FCS file-writing software? It is anything that creates an FCS file: cytometer acquisition software, post-processing tools, analysis applications with export functionality, etc.

FCS files may not conform to ISAC specification for a number of reasons:  for example, file truncation during upload with slow or transient internet connections, and post-processing or export utilities that write files. To help users verify or assess which files could potentially have issues, we have implemented quality indicators that mark files with associated warnings. We now flag files that are likely to be missing data with a red icon (), and show “info warnings” () for files that have other header nonconformities such as missing keyword information. We advise users to not proceed with analysis using files marked with the red icon, whereas files with “info warnings” are likely safe. Read more on our support site about how these warnings manifest and the steps you should take if you see one of these indicators next to your files.

We are committed to pushing forward flow cytometry standards and are always looking to augment our approach, so please don’t hesitate to contact us with questions.

– Angela and the Cytobank Team