Summary plot problems

[Cheng Li]

--- Old discussion messages ---

Posted: 14 Nov 2008 01:36 pm Post subject: Summary plot problems

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Dear Dr. Li,

Whenever I use the summary plot, it would always show 100% of my
samples having areas of high or low copy number. This does not change
even when I set different threshold values. I'm analyzing about 80
samples, and it seems that at most ~60% of samples have low copy
numbers in a certain region, but the summary plot would always display
this region as affected in 100% of samples. Am I doing something
wrong?

Thanks,
Khanh Thieu


lch Posted: 14 Nov 2008 05:26 pm Post subject:

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Make sure you set copy number min and max at "options/score" for
single sample curve type.

Cheng


Posted: 17 Jun 2008 09:39 am Post subject: Summary Plot cannot show
CN and LOH at the same time

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Dear Dr. Li :

You originally designed a new summary plot function which can show CN
and LOH at the same time. However, this function was lost in newer
version (May and June). Could you fix it?

Chueh-Chuan Yen


lch Posted: 25 Jun 2008 06:22 pm Post subject:

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In the current version, if "Chromosome/Show LOH in copy" is checked,
"Summary plot" will draw UPD proportions alone in a figure. Do you
think it's better to plot UPD and copy number data together?

Cheng


lch Posted: 27 Jun 2008 03:15 pm Post subject:

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Please try this updated version to plot UPD in the copy number summary
plot and for larger vertical size:

Http://biosun1.harvard.edu/~cli/dchip.exe

Cheng


Sent: Wednesday, June 25, 2008 11:01 PM
To: Cheng Li
Subject: Re:

Dear Dr. Li:

Please see the two attached files
Feb version can show CN and LOH at the same time, which can give a
pretty good view of regions with corresponding LOH and reduced CN

However, in June version, summary plot can show either CN or LOH, but
cannot show them at the same time.

Also the exported figure in June version seems larger, which is not
suitable for publications.

Chueh-Chuan Yen

Posted: 25 Feb 2008 06:38 pm Post subject: Summary plot for LOH

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Dear Dr. Cheng:

Is it possible to add a function called " Summary plot for LOH", just
like now we have for copy number? Because for current "LOH score", I
did think it could point out the region of high prevalence of LOH.

BTW, could you add back the "show LOH in copy view" function? I think
it is quite good, but I cannot find it in new version.

Thanks a lot

Chueh-Chuan Yen


ccyen Posted: 25 Jun 2008 11:13 am Post subject: Summary plot

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Dear Dr. Li:

Several error in summary plot:
(1) The new version of summary plot lost the function of showing both
CN and LOH at the same time.
(2) The size of the plot is a little bit larger than previous one. It
is too big for publication purpose
(3) I used a gene list function and use summary plot. But it seems
that the position of these genes is shifting, that is, not in the
correct position. Could you fix it?


mayagao Posted: 06 Oct 2007 07:15 pm Post subject: About Copy
number summary plot

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Hi Cheng,

I am curious about why I cannot get the Copy number summary plot.
Seems that "Copy number summary plot" was disabled. I am including two
snapshots for your reference.

Thanks!

Alex


lch Posted: 07 Oct 2007 08:10 pm Post subject:

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You can use key 'D' to switch to copy number view (instead of log2
view) to activate the menu.



Diana Posted: 09 Jul 2007 10:55 am Post subject: Copy number
summary plot crashed

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When I try to make a copy number distribution plot at the inferred
copy number view the program crashes. I am analyzing 250 cases
compared to 750 controls with the Affy 500K mapping array. This
happens whether I use the dchip2006latest or dchip2007_04. Is my data
set too big? Any advice?


lch Posted: 11 Jul 2007 06:09 pm Post subject:

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Thanks for reporting the issue. This bug is due to that "Open group/
Options/Load probe data in memory" is unchecked and the "Plots" icon
on the left is not displayed.

Please use this 7/11 version to correct the issue:
http://www.hsph.harvard.edu/~cli/dchip2006.exe