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
Thanks again for helping us improve Galaxy...
On Mon, Jul 18, 2011 at 10:52 PM, Alison Harrill <AHarrill(a)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.
From: Ross [mailto:email@example.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
> 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
> know if you see an obvious workaround.
> Thank you,
> 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:firstname.lastname@example.org]
> 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
>> Hi, Ross,
>> Thanks so much for kindly following up with me. I tried the
>> you suggested, but it appears to not be working for me.
>> prompts me to save a file called display.htm and when I open the
>> it just reads "Unable to remove temporary library download archive
>> Best wishes,
>> -----Original Message-----
>> From: Ross [mailto:email@example.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?
>> On Sat, Jul 16, 2011 at 9:39 AM, Ross <ross.lazarus(a)gmail.com> wrote:
>>> Hi, Alison,
>>> Thanks for reporting this error - I just confirmed that you have
>>> 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
>>> and can be saved - eg on a PC or linux workstation, while hovering
>>> over the '(Click to download image Armitagep_manhattan.png)' press
>>> right side mouse button and choose "save link as.." - you will be
>>> to choose a location to save the image file on your local
>>> I hope this "work around" allows you to get on with your work -
>>> for the inconvenience and thanks again for finding and reporting
>>> error - we will fix it as soon as we can.
>>> On Sat, Jul 16, 2011 at 6:46 AM, Alison Harrill
>> <AHarrill(a)thehamner.org> wrote:
>>>> I have a question about generating a Manhattan/QQ plot using the
>> tool. I
>>>> was able to successfully run the plot (the result box is green),
>> when I
>>>> try to download the results, I get a message that says "Unable to
>>>> temporary library download archive and directory." Is there another
>> way to
>>>> retrieve the data?
>>>> Thank you,