Hi Tuuli and all.
This is a bit disappointing but I see quite some openings for appeal / resubmission.
I think what should be stressed more in the novelty is the transcript resolution that we obtain. Therefore, I also agree that addressing transcript ratio QTLs in more detail will help.
The transcript ratio thing: I think this is because you calculate transcript ratios. When you put all the transcript abundances in one
model with an additional factor for overall expression and subsequently estimate the coefficients of the individual transcripts, you will have higher power. Is that something that can be done?
The status of the other paper is still “under consideration”. It has not changed since January 4. Should I email the editor? I guess
the review process is independent from that of the main paper, and I do not need to refer to the main paper in that email, right?
My flight on Thursday is at 4.50 pm CET. I may join for a few minutes.
Perhaps we can already schedule a next TC on Thursday 31 at 4 pm CET to discuss some more issues that I brought up.
Best
Peter
From:
geuvadis_rna_analysis-bounces@lists.crg.es [mailto:geuvadis_rna_analysis-bounces@lists.crg.es]
On Behalf Of Tuuli Lappalainen
Sent: Tuesday, January 22, 2013 8:37 AM
To: Manolis Dermitzakis;
Subject: [Geuvadis_rna_analysis] RNAseq paper
Dear all,
The Geuvadis RNAseq paper was rejected this morning. We've decided with Manolis that we should make an appeal, and we have already been in touch with
Since we were going to have a call soon anyway, let's have a TC on Thursday the 24th at 4pm CET. Before that, I'd be happy to hear your
comments to the response letter (deadline: immediately). There's a couple of bigger items to discuss, and specific questions to a few of you - see below. There won't be a lot of new analysis to do if we're given
the chance to revise.
Questions:
- Do we drop non-essential analyses as #2 suggests? This would mean RNA editing, maybe fusions and subtle splicing. I'm not keen to, but if people think it would improve the overall quality of the paper...
- Should we restructure the supplement by topic instead of methods/figures/tables? Need to ask
- Andrew & Natalja: Can we add a data slicing and download function to the browser (or a separate site linked from the browser)?
- Jean & Mar: How is the qualitative/quantitative analysis affected by low-abundance transcripts? Will the results change if the threshold is different?
- Jean, Mar, Pedro, Micha (and myself): #2 raises an important question (really!): most of transcript variation is explained by transcript ratio differences, but we find very few QTLs for this. Why do you think this is? Is all that variation really just random/environmental/epigenetic?
- Jean: #3 suspects that the 3% of transcriptome variation explained by population could be just random - how do we respond to this?
- Manny: What could we do to add novelty value to NMD analysis?
- Gabrielle: Is it possible to make a read-only password for the wiki? We could give one to the reviewers just so that they can see it.
best regards,
Tuuli
--
Tuuli Lappalainen, PhD
Department of Genetics, Stanford University School
Department of Genetic Medicine and Development, University of Geneva
Email: tuuli.e.lappalainen@gmail.com / tlappala@stanford.edu
Tel: +1 415 351 9713
Bustamante lab
Department of Genetics