Nicola Romanò @nicolaromano@qoto.org

@failedLyndonLaRouchite @ethanwhite definitely not Hons projects...

Just reading this very interesting paper on how many #replicates are needed for appropriate analysis of bulk #RNAseq data and comparing tools for DE gene expression.

#bioinformatics #article #goodread

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878611/

From the abstract

With three biological replicates, nine of the 11 tools evaluated
found only 20%–40% of the significantly differentially expressed (SDE) genes identified with the full set of 42 clean replicates.
This rises to >85% for the subset of SDE genes changing in expression by more than fourfold. To achieve >85% for all SDE genes regardless of fold change requires more than 20 biological replicates.

@clathrin @richardsever Let me tell you a story about data reuse

I have a student who wants to re-analysing some sequencing data from a paper.

1. Paper reports the data will be shared on GEO at the time for publication. No GEO ID is present, although the paper has been published for a while now.

2. After digging onto GEO for longer than needed (it always feels like I'm back in the 90s on MySpace), I find the data. Well, part of it, the rest is nowhere to be found.

3. Several emails to the authors, no reply

4. In the meantime we manage to find the data. I confirm my hate for GEO.

5. Data is from human patients, which the paper indicates as patient 1,2,3 etc.
The patient numbers in the deposited data only partially match those in the paper. Luckily we're pretty confident we can tell who's who but still...
Data from one patient (out of 6) is missing

6. Out of three set of experiments, data is available only for two, the other are missing

The student has pretty much finished her project.
We're still waiting for the authors to reply to our emails.

I have to say, I've had much better experience with other papers, but still, I think we're a long way to have properly archived data.

@igutierrez@mastodon.social What do you edit PDF with though? Nowadays if I'm working with other people I use Google Docs. Formatting stays correct (not the case when going between Word/OpenOffice/LibreOffice esp with different OS), I can add comments and suggestions, have revision tracking, and can work synchronously with colleagues.
I'm not sure you can really do that with PDF, but I'll be super happy to be corrected.

@mcaleerp I enjoy marking certain assessments, hate marking others.

It mostly depends on the assessment, there's a lot of badly designed ones around unfortunately.

@gringene ooohhh I remember dismembering an old toy to get the motor out. Lots of fun! I was using it with Meccano rather than Lego though.

I also remember that at the time it sounded like the most interesting thing to do what's connecting the motor to the mains. I am sure your kids will be wiser, that didn't end well for the motor, although I had a nice pyrotechnics show in my room

@nancylwayne @Frederik_Borgesius I think the main problem is not that there are people cheating. It's that universities don't do anything about them, and it's not just when they are 'big' scientists (well, they enabled them to become directors or what not)

Having seen a couple of cases of this, my impression is that the policy of many universities is to cover their assess and not do anything about 'problematic' employees, whether they falsify data, or harass others. It doesn't make sense, because I'd rather work for a uni that said 'we made a mistake hiring X, we will not support this person or their science anymore'. But apparently that's bad PR. 😭