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(a)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; geuvadis_rna_analysis(a)lists.crg.es
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 Magdalena about this.
We'll need to send her a response letter in a couple of days (see the attachment with
reviewer's comments and a rough response draft). It ain't over til it's over.
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 Magdalena too.
- 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 of Medicine , and
Department of Genetic Medicine and Development, University of Geneva
Email: tuuli.e.lappalainen@gmail.com<mailto:tuuli.e.lappalainen@gmail.com> /
tlappala@stanford.edu<mailto:tlappala@stanford.edu>
Tel: +1 415 351 9713
Bustamante lab
Department of Genetics
300 Pasteur Dr. Lane L301
Stanford, CA 94305-5120
USA