> A similar question was asked some time ago. Here is a link to the
> answer.
> http://www.mail-archive.com/basedb-devel@lists.sourceforge.net/msg00062.html
Thanks Nicklas,
Sorry I should have done a search - this thread was in my vacation backlog...
So we have the same problem and I should take a look at BASE2.5 to see if
keeping the raw data file helps.
Vegard, did you come up with a work-around? Should one import all data
"straight" and use the dyes as a proxy for the channel number? If raw
bioassays are annotated as "dye-swap" would one need to create a ratio formula
that did something like this:
if(rawbioassay.isAnnotated("dye swap", true), ch(2)/ch(1), ch(1)/ch(2))
Otherwise I don't see a convenient way to view/analyse an experiment with dye
swaps.
Any experiment where both samples (in a two-colour expt) are annotated
with something relevant (i.e. male vs. female rather than male vs. pooled
control) it is rather critical to know which channel goes with which sample.
I know that neither BASE1 nor BASE2 have been designed to display the
annotations of dual-annotated bioassays (e.g. male vs female) but in BASE1 the
info was all there in the database.
Has this not been an issue with Tab2Mage import -> export?
Is the hyb.getCreationEvent().getSources() query guaranteed to return
l.extracts in any particular way? Perhaps in the order they are added
to the database?
cheers,
Bob
Nicklas Nordborg writes:
> vegard nygaard wrote:
> > Hi. I am searching for some information in BASE2 that I often looked at in
> > BASE1. I can't find it. Can you help me? This is not a migration question.
> > The BASE2 data is fresh test data.
> >
> > I have a Raw bioassay and want to see what raw data file I used to create
> > it. I can't trace that info anywhere in the BASE2 GUI or in the API. Where
> > is that information hidden?
>
> This information is not stored (*). For BASE 2.5 we are working on a
> generic solution for attaching files to various items (raw bioassays,
> array designs, etc), and also an option to keep the data in the files
> instead of importing it into the database. This is how it currently
> works for Affymetrix data, but the solution can't be extended to cover
> other formats. For more info see http://base.thep.lu.se/ticket/721.
>
> > And what happens to the raw data file when it is used to make a raw
> > bioassay. In BASE1 I think it was automatically copied to another place and
> > you could actually delete it from upload, but it would still be there
> > accessible from the raw bioassay page. The downside of this was a lot of
> > double storage. How is this handled in BASE2?
>
> Nothing special happens to the file.
>
> > A common BASE1 user error is mixing up what is in ch1 and ch2.
> > In problem solving, I often want to see what file format I used to parse
> > that raw file into a raw Bioassay. I can't find that information in BASE2.
> > Where is it?
>
> It is not stored (*).
>
> > Also i want to see what sample I assigned to ch1 and ch2. I could not find
> > this information in BASE2.
>
> The link to samples was mainly used for getting access to annotations in
> the analysis part. In BASE 2 the annotation system is very different
> from the BASE 1 annotation system, and the link to samples has been
> replaced with (inherited) annotations at the raw bioassay level.
>
> > And when I make a new hybridization and adding
> > two samples, I am not forced to assign the labeled extracts to channels as
> > in BASE1. What is the definition of ch(1) and ch(2) in BASE2?
>
> I don't think there is any.
>
> > How do I now that my ratio is A/B and not B/A?
>
> The ratios are calculated with Formula items. BASE ships with a formula
> for calculating ch(1) / ch(2) but it is easy to change that or create
> another formula which instead does ch(2) / ch(1).
>
> /Nicklas
>
> (*) The information is stored as parameters to the job that imported the
> data but there is no way to easily query that information. In theory you
> can check all jobs which involved running an import plug-in and had a
> specific raw bioassay as one of it's parameters. Then, check the other
> parameters for info about file, file format, etc. Since jobs can be
> deleted, this would not be a very stable solution...
>
>
>
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--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
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