Hi, Alison

I've made some fixes to the Manhattan/QQ tool (galaxy-central revision
#dacf97a6c663) so it now handles your data - thanks again for
discovering these edge cases - the revised code is now available and
working on http://test.g2.bx.psu.edu/ where your data produces plots.
In particular X in your data, and for good measure Y and Mt are now
translated into 23,24 and 25 respectively so the code can now cope
with those inputs and they should appear in linear order in the
Manhattan x axis

The floppydisk link (download) problem remains to be fixed as it's
more complex. We only update the main server every few weeks so the
changes I just made will take a while to appear there. Meanwhile,
please try the revised tool by making yourself an account and then
uploading your data to http://test.g2.bx.psu.edu/ - please let me know
how you get on?

Of course, the (?FDR adjusted) p values in your data are a challenge -
typically, the Manhattan and QQ plots are run with unadjusted p values
which are expected to be distributed uniformly 0-1 under the null...
FYI, when I use the grouping tool on your data, I see that chromosomes
20,21 and 22 are absent from the file - is this expected? Group with a
count gives:

1       22910
10      9990
11      12764
12      13413
13      13068
14      11319
15      11175
16      8483
17      12017
18      10073
19      6927
2       18332
3       16173
4       15401
5       15259
6       15487
7       15217
8       12485
9       14560
X       3951

Thanks again for helping us improve Galaxy...

On Mon, Jul 18, 2011 at 10:52 PM, Alison Harrill <aharr...@thehamner.org> wrote:
> The first time I uploaded the file, I loaded in the -logP values
> instead. After that, I changed the file to raw p values and reuploaded.
> Do you think it would help to upload the file again, but change the
> filename? I just wonder if that original file didn't get cleared out.
>
> Alison
>
> -----Original Message-----
> From: Ross [mailto:ross.laza...@gmail.com]
> Sent: Monday, July 18, 2011 8:51 AM
> To: Alison Harrill
> Subject: Re: [galaxy-bugs] Error message when trying to dowload
> Manhattan plot using the web version
>
> ok - thanks. These are not raw pvalues and your data is definitely
> causing the Manhattan plot to fail.
>
> This will take me a little time to figure out - I'll get back to you
> in a day or two - thanks again for reporting this problem
>
> On Mon, Jul 18, 2011 at 10:16 PM, Alison Harrill
> <aharr...@thehamner.org> wrote:
>> Good morning,
>>
>> Sorry for taking a while to get back to you (I was out of town for the
>> weekend). I set permissions to share the dataset with you. Please let
> me
>> know if you see an obvious workaround.
>>
>> Thank you,
>> Alison
>>
>>
>> Alison Harrill, Ph.D.
>> Research Investigator
>> Institute for Drug Safety Sciences
>> Hamner Institutes for Health Sciences
>> phone: (919) 226-3142
>> fax: (919) 226-3150
>>
>>
>>
>> -----Original Message-----
>> From: Ross [mailto:ross.laza...@gmail.com]
>> Sent: Sunday, July 17, 2011 7:25 AM
>> To: Alison Harrill
>> Subject: Re: [galaxy-bugs] Error message when trying to dowload
>> Manhattan plot using the web version
>>
>> Can you please share a history with me (use this email address) so I
>> can take a look please?
>>
>> I'm talking about links on the results page where you (should!) see
>> some graphs - when you click the history item display ('eye') icon -
>> not the history item save ('floppy disk') icon
>>
>> On Sun, Jul 17, 2011 at 9:15 PM, Alison Harrill
> <aharr...@thehamner.org>
>> wrote:
>>> Hi, Ross,
>>>
>>> Thanks so much for kindly following up with me. I tried the
> workaround
>>> you suggested, but it appears to not be working for me.
> Right-clicking
>>> prompts me to save a file called display.htm and when I open the
> file,
>>> it just reads "Unable to remove temporary library download archive
> and
>>> directory".
>>>
>>> Best wishes,
>>> Alison
>>>
>>> -----Original Message-----
>>> From: Ross [mailto:ross.laza...@gmail.com]
>>> Sent: Sunday, July 17, 2011 4:09 AM
>>> To: Alison Harrill
>>> Subject: Re: [galaxy-bugs] Error message when trying to dowload
>>> Manhattan plot using the web version
>>>
>>> Hi, Alison - I wanted to be sure you are able to get your images from
>>> the tool - the proper fix is going to take a while so I hope those
>>> links are working for you?
>>>
>>> cheers...
>>>
>>>
>>> On Sat, Jul 16, 2011 at 9:39 AM, Ross <ross.laza...@gmail.com> wrote:
>>>> Hi, Alison,
>>>>
>>>> Thanks for reporting this error - I just confirmed that you have
>> found
>>>> a bug - the download function is currently not working correctly for
>>>> composite datatypes in the history.
>>>>
>>>> Fortunately, the images themselves have download links under each
> one
>>>> and can be saved - eg on a PC or linux workstation, while hovering
>>>> over the '(Click to download image Armitagep_manhattan.png)' press
>> the
>>>> right side mouse button and choose "save link as.." - you will be
>> able
>>>> to choose a location to save the image file on your local
>> workstation.
>>>> I hope this "work around" allows you to get on with your work -
> sorry
>>>> for the inconvenience and thanks again for finding and reporting
> this
>>>> error - we will fix it as soon as we can.
>>>>
>>>>
>>>>
>>>> On Sat, Jul 16, 2011 at 6:46 AM, Alison Harrill
>>> <aharr...@thehamner.org> wrote:
>>>>> Greetings,
>>>>>
>>>>> I have a question about generating a Manhattan/QQ plot using the
> web
>>> tool. I
>>>>> was able to successfully run the plot (the result box is green),
> but
>>> when I
>>>>> try to download the results, I get a message that says "Unable to
>>> remove
>>>>> temporary library download archive and directory." Is there another
>>> way to
>>>>> retrieve the data?
>>>>>
>>>>> Thank you,
>>>>>
>
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