0 vs 1 Tech replicates problem in the dataProcess function

[Ayman REFFAI]

Hey everyone, 

In the output data of the dataProcess function, I get 0 in the Tech. replicates for the 21 control samples, and 1 for the 41 disease samples (see screenshot 1) knowing that both don't have any tech replicates so the correct number should be 1, right? 

With another dataset, I got 0 in the tech. replicates for both controls (15) and disease samples (9) knowing that I don't have any tech replicates in the study (see screenshot 2).

The only common trait among samples with 0 tech replicates in the dataProcess output is that they're fractionated samples. 

I am wondering if it's normal to get 0 for fractionated samples or if there's something I need to change in order to get 1 (which is the usual normal).

Thank you!

Best,

Ayman Reffai

[Mateusz Staniak]

Hi,

last time this potential bug was reported I wasn't able to reproduce it. Could you kindly share a small subset of data that reproduces it?

Kind regards,

Mateusz

[Mateusz Staniak]

Hi,

we compute the number of tech replicates in this output as a rounded proportion of Runs to (BioReplicates multiplied by Fractions) within Condition.
Your annotation looks correct and this text output does not affect other computation.
Tech. rep. counts are different because Runs are counted after their labels were altered to account for fractions, while number of fractions does not change. Frankly, this is old code and I'm not sure what the intention was. I will talk about this to the team and it will either stay like that with better documentation or we will change the method of counting.

Kind regards,
Mateusz