Bug in the plot lanes tool?

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Bug in the plot lanes tool?

John Alexander-7
Greetings list,

I've had this difficulty off and on for a while and I think I have
isolated the specific problem, i.e. I can now reproduce the problem.

The plot lane tools only seems to work on images that have not been B&C
adjusted.

If I load my tiff of my blot and outline the lanes 1,2,3 ... etc, it
works fine.  The problem is that some of my bands are very very faint in
comparison to other strong ones, so, I adjust the contrast so I can see
the faint ones.  I then outline the lanes again, and when I plot them,
the resulting plot is blank.  If I then go to B&C and "reset" the image,
it works again.


John
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Re: Bug in the plot lanes tool?

Jonathan Hilmer
I see the same behavior, specifically with the Gel Analyzer (but not
Plot Profile), using version 1.39u.


Jonathan

On Mon, Mar 31, 2008 at 12:16 PM, John Alexander <[hidden email]> wrote:

> Greetings list,
>
>  I've had this difficulty off and on for a while and I think I have
>  isolated the specific problem, i.e. I can now reproduce the problem.
>
>  The plot lane tools only seems to work on images that have not been B&C
>  adjusted.
>
>  If I load my tiff of my blot and outline the lanes 1,2,3 ... etc, it
>  works fine.  The problem is that some of my bands are very very faint in
>  comparison to other strong ones, so, I adjust the contrast so I can see
>  the faint ones.  I then outline the lanes again, and when I plot them,
>  the resulting plot is blank.  If I then go to B&C and "reset" the image,
>  it works again.
>
>
>  John
>
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Re: Bug in the plot lanes tool?

John Alexander-7
I am using 1.40b - but I am certain this has been going on since version
1.38.

So far, I can adjust the contrast, outline the lanes, plot the profile
(which is blank), then reset the contrast, then Analyze->Gels->Re-plot
lanes and I get the correct plot.  Annoying, but at least it works.

One other thing I find slightly annoying is that the plots are 8-bit.
This is an issue when comparing bands when there are both strong and
weak bands.  I find myself having to plot the lanes of strong bands
first, then plot the lanes of the weak bands.  To compare the strong and
the weak, I have to plot a middle strength band with both the strong and
the weak, and determine a "scaling" factor.  It would be nice if the I
were able to simply plot all the lanes and not have a "strong" signal
reduce a weak signal to nothing.  I figure that would be done by using a
32-bit plot lanes algorithm.

(I think this hasn't been much of an issue in the past because
chemiluminescence usually didn't provide a decent dynamic range, but
fluorescent westerns are easily providing 4 orders of magnitude - well
beyond the 8-bit limit.)




Jonathan Hilmer wrote:

> I see the same behavior, specifically with the Gel Analyzer (but not
> Plot Profile), using version 1.39u.
>
>
> Jonathan
>
> On Mon, Mar 31, 2008 at 12:16 PM, John Alexander <[hidden email]> wrote:
>> Greetings list,
>>
>>  I've had this difficulty off and on for a while and I think I have
>>  isolated the specific problem, i.e. I can now reproduce the problem.
>>
>>  The plot lane tools only seems to work on images that have not been B&C
>>  adjusted.
>>
>>  If I load my tiff of my blot and outline the lanes 1,2,3 ... etc, it
>>  works fine.  The problem is that some of my bands are very very faint in
>>  comparison to other strong ones, so, I adjust the contrast so I can see
>>  the faint ones.  I then outline the lanes again, and when I plot them,
>>  the resulting plot is blank.  If I then go to B&C and "reset" the image,
>>  it works again.
>>
>>
>>  John
>>
>

--
John K. Alexander, Ph.D.
Post-Doctoral Fellow
William Green Laboratory
University of Chicago
Dept. Neurobiology, Pharmacology, and Physiology
947 East 58th Street
Abott Hall 402
Chicago, IL 60637
(off) 773-702-9386
(fax) 773-702-3774
[hidden email]