Great using 1 worked!
Thanks
From: Nicklas Nordborg
To: BASE ML
Sent: Sunday, 8 February, 2009 22:58:08
Subject: Re: [base] Lowess normalisation - Block parameter
Louise Donnison wrote:
> Hi
> I have been trying to normalise with block size 48 usi
Louise Donnison wrote:
> Hi
> I have been trying to normalise with block size 48 using the Lowess
> normalization plugin. It does not appear to work for me.
> It gives the same result as if I use block size 0.
If your array has 48 block on it this is the expected behavior. The
parameter tells the
Hi
I have been trying to normalise with block size 48 using the Lowess
normalization plugin. It does not appear to work for me.
It gives the same result as if I use block size 0.
I have been looking at LowessNormalisation code.
The spot spot data is ofsize 17328 split over 48 blocks.
When the cod
The problem is now being fixed, http://base.thep.lu.se/ticket/1077.
Unfortunately this problem affects all versions of BASE2 and everyone
are recommended to upgrade to the future 2.7.2 (or later).
The problem is localized and 2.7.2 will be released later today or at
latest tomorrow. More detail
Thanks very much Jari. Sorry I didn't have time to look deeper and figure out
what was wrong. As you'll see in a few weeks we have a big project nearing
release.
cheers,
Bob.
Jari Häkkinen writes:
> Hi Bob,
>
> We are looking into the issue. It looks like the BASE2 version of lowess
> is
Hi Bob,
We are looking into the issue. It looks like the BASE2 version of lowess
is flawed. We are testing and reading publications to make sure that we
make a proper fix. We already have a fix for the problem but want to
make sure that we don't create new bugs. We plan to release a 2.7.2 ASAP
I've done some more tests on the lowess problem.
Please refer from now on to our development server:
http://base.vectorbase.org:8080/base2dev/
Experiment: "Male vs. female (Koutsos et al., 2007)"
I ran the base1 lowess plugin and got a very different result compared to the
base2 plugin. The b
Has anyone had problems with the Lowess analysis plugin?
To me it looks like it is overcorrecting. Where a M/A plot
is largely below the zero line before normalisation, it ends
up largely above it afterwards.
I'm using default values (including 0 for block group size).
Default values were alway
