Specify cdf library and annotation?

[MPM]

I'm not sure what I'm doing wrong. I'm trying to analyze some cel
files. When I ran AltAnalyze the first time it asked me to specify
the cdf library and annotation file. I mistakenly specified U133 Plus
2.0 when I should have used U133 2.0 (no "Plus"). Naturally it
failed, with an error something like "unexpected cel file type".

Realizing my mistake, I tried again. Now, when I try to analyze the
data it doesn't ask me what cdf or annotations to use-- it defaults to
the wrong ones I used the first time. This happens with AltAnalyze v1
and v2. I've tried renaming my project, the folder the files are in,
and even restarting the computer. How do I correct this?

Mike

[Nathan Salomonis]

Hi Mike,

This issue should fixed in the latest, version 2.03, which has better array determination built-in. You can always download the latest version, extract it and then simply replace it's AltDatabase directory with the one from the old version, if you want to skip re-downloading the database all together.

To fix this problem in an older version you just need to edit the file ArrayFileInfo.txt in the Config folder and delete the row which has your custom array annotation added.

Best,
Nathan

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[MPM]

After trying the new version, I get this error I haven't seen before:
Traceback (most recent call last):
File "AltAnalyze.py", line 5867, in <module>
File "AltAnalyze.py", line 4481, in AltAnalyzeSetup
File "UI.pyc", line 2475, in getUserParameters
File "AltAnalyze.pyc", line 4481, in AltAnalyzeSetup
File "UI.pyc", line 2745, in getUserParameters
File "UI.pyc", line 300, in write
File "UI.pyc", line 301, in set
File "Tkinter.pyc", line 911, in update
_tkinter.TclError: can't invoke "update" command: application has
been destroyed

This is after specifying my cdf and annotation files. What's going
on?

On Jul 1, 1:51 pm, Nathan Salomonis <nsalomo...@gmail.com> wrote:
> Hi Mike,
>
> This issue should fixed in the latest, version 2.03, which has better array determination built-in.  You can always download the latest version, extract it and then simply replace it's AltDatabase directory with the one from the old version, if you want to skip re-downloading the database all together.
>
> To fix this problem in an older version you just need to edit the file ArrayFileInfo.txt in the Config folder and delete the row which has your custom array annotation added.
>
> Best,
> Nathan
>

[MPM]

Hmm... I manually copied the csv and cdf files to the appropriate
folders under AltAnalyze
C:\Documents and Settings\Administrator\Desktop\AltAnalyze_v.2.0.3-
Win32\AltDatabase\affymetrix...
instead of specifying another directory. Now it seems to be analyzing
my data.

Fingers crossed.

[MPM]

That did it. I'm not sure why.

[Nathan Salomonis]

I downloaded the same files as you and it worked the first time, after
specifying the local CDF and CSV files. These kind of issues sometimes
highlight some bug that requires very specific and random things to go
wrong and hence are hard to track down.

You are definately right in that if you had selected the wrong CDF
here, it would keep referring to that, even in the new version. The
only way to address this now is by editing that ArrayFileInfo.txt
file.

Best,
Nathan