The Pipeline - Comments

Christine Hoogland comments on How Excel shapes the world

Christine Hoogland — Wed, 17 Apr 2013 01:42:05 +0000

Definitely not off topic, there was even a publication in 2004 highlighting this issue for gene names transformed into dates (http://www.biomedcentral.com/1471-2105/5/80). Even sadder, it has been found very recently in a major database (Cancer Genome Atlas), see http://nsaunders.wordpress.com/2012/10/22/gene-name-errors-and-excel-lessons-not-learned/

Torsten Seemann comments on Welcome Benita Vincent

Torsten Seemann — Thu, 28 Mar 2013 22:05:16 +0000

Welcome to the team Benita! Sorry I missed speaking to you at the FOAM conference, hopefully we can meet some time soon.

wade hines comments on Don't correlate proportions!

wade hines — Mon, 25 Mar 2013 04:30:01 +0000

It's true that many don't really think through all of the various normalization steps being applied to data.
Is the gross level of transcription higher in one state than in another?
Are we normalizing to total transcript or to a housekeeping subset of largely invariant transcripts or to some particular reference set? These questions impact every time of analysis including for instance ANOVAs. But that does not mean we can't use ANOVAs.
For just about everything done we quickly run into trouble if we are comparing two states that are significantly different. A functionally equivalent level of transcript can be shifted to be apparently smaller in a statistically significant way if there is a large increase in abundant transcripts if we normalize to total transcript levels. Every analysis needs to be thought through. This is one good reason we can't reliably outsource bioinformatics to BGI.

David Lovell comments on Don't correlate proportions!

David Lovell — Mon, 25 Mar 2013 03:54:20 +0000

"The video presents an absurdity where one infers absolute numbers from correlations of proportionality."
...well I think a lot of folks are doing that with omics data, especially transcriptomics and metagenomics.

I guess I just don't understand how to _interpret_ correlations of relative abundances.

wade hines comments on Don't correlate proportions!

wade hines — Mon, 25 Mar 2013 03:45:19 +0000

No no no no no. There's nothing wrong with correlating relative abundance data, or proportional data.
The video presents an absurdity where one infers absolute numbers from correlations of proportionality. That is of course wrong but that does not mean one cannot usefully correlation proportionality. The point in in how you interpret any correlations or lack of correlations observed.

By the same token, linear correlations are not necessarily more meaningful than rank order correlations (Spearman). By all means, think about the tool you are using and what relationships are implied. Don't make teh stupid leap the video refers to, inferring absolution trends from proportional trends, but don't throw away a tool just because somebody can imagine a way to use it incorrectly.

Nick Wong comments on Don't correlate proportions!

Nick Wong — Fri, 22 Mar 2013 07:12:14 +0000

do you have a tool David for this? I was sold and it would be awesome for me to have a look at our methylation data, because I know it's all proportions for a fact as all methylation is measured in % !!

David Lovell comments on I know what you did last (BioInfo)Summer

David Lovell — Wed, 12 Dec 2012 02:09:15 +0000

And they were!
On a more positive note, AMSI are capturing the BioInfoSummer 2012 vibe with a great photo gallery.

Virginia Tressider comments on I know what you did last (BioInfo)Summer

Virginia Tressider — Tue, 11 Dec 2012 22:25:00 +0000

Your hopes for the in-flight meal were, of course, doomed to be crushed.

Torsten Seemann comments on Share your slides through the Australian Bioinformatics Network

Torsten Seemann — Wed, 24 Oct 2012 10:30:03 +0000

I'm a bit strapped for time right now, but if you think adding any of my CC-licenced slides from my website here http://www.vicbioinformatics.com/documents.shtml would be useful, then please go ahead and add them on my behalf to the ABN SS account. Torsten.

Nathan Watson-Haigh comments on Request for comment: ABN Connection Grants

Nathan Watson-Haigh — Thu, 04 Oct 2012 21:20:36 +0000

I think this is a brilliant idea!

I'm excited by this because much of this aligns nicely with what we are trying to do with BIG SA. Having the opportunity to get funding for local bioinformatic events would be extremely helpful!

I echo Torsten's comments regarding being open. With Australia being a pretty small bioinformatics player, in global terms, and being geographically distant from each other, I think it is vitally important that we are able to access this level of information to strengthen the national bioinformatics community.

I also support Torsten's comments about funding domestic travel for international visitors, especially for those states which might otherwise find it more difficult to attract such visitors on their own. To facilitate this I would like to request the establishment of some sort of mechanism whereby these visitors are publicised more openly. This would then allow such domestic travel to be arranged. This may be as simple as advertising the fact you have someone visiting or maybe something more elaborate.

I assume that by saying the grants will support "meetings" this also means hosting of "events" more generally that fit within the scope of what the ABN is all about?

Good stuff!
Nathan