Every few months I tell myself I need to pay better attention to what those smart people in ABRF are doing. Unfortunately, it tends to slip down my
Point in case: This awesome analysis ABRF is doing right now! The study is called "Differential Abundance Analysis in Label Free Quantitative Proteomics". I should probably stop to read the whole thing but I won't have time until
If you are interested you'll probably want to download these now, cause we know how long an analysis of this type tends to take!
Shout out to Brett Phinney for sending me an email tipping me off to this pending deadline!
"Therefore, peptide identifications that can be assigned to multiple proteins should be ignored. Such identifications have already been removed from the provided files."
ReplyDeleteThese proteins can sometimes be estimated quite accurately, if they're shared with another protein that has unique peptides. It's a shame they've assumed that they are too difficult to use.
Hello Ben,
ReplyDeleteThey included only technical replicates (3) for the analysis and no biological ones. This unfortunately prevents you from doing proper t-test or anova based statistics and limits you to rather simple FC vs intensity statistics.
I would say that is a poorly designed study for the purposes of evaluation of LFQ algorithms and downstream differential analysis statistics.
I.