Re: [galaxy-dev] [galaxy-bugs] Error message when trying to dowload Manhattan plot using the web version
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 <AHarrill@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.lazarus@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
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.lazarus@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
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.lazarus@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.lazarus@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
On Sun, Jul 17, 2011 at 9:15 PM, Alison Harrill <AHarrill@thehamner.org> wrote: 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
On Mon, Jul 18, 2011 at 10:16 PM, Alison Harrill <AHarrill@thehamner.org> wrote: this
error - we will fix it as soon as we can.
On Sat, Jul 16, 2011 at 6:46 AM, Alison Harrill <AHarrill@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,
Hello Alison, I wanted to share with you the bitbucket ticket for the improvements to composite datatypes. As Ross described, this would be part of a larger project. The ability to save composite data using the floppydisc icon would be one example an impact of the proposed change. https://bitbucket.org/galaxy/galaxy-central/issue/654/improvements-for-compo... Thanks again for the feedback and use case example, Best, Jen Galaxy team On 7/19/11 8:44 PM, Ross wrote:
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<AHarrill@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.lazarus@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
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.lazarus@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
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.lazarus@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.lazarus@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
On Sun, Jul 17, 2011 at 9:15 PM, Alison Harrill <AHarrill@thehamner.org> wrote: 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
On Mon, Jul 18, 2011 at 10:16 PM, Alison Harrill <AHarrill@thehamner.org> wrote: this
error - we will fix it as soon as we can.
On Sat, Jul 16, 2011 at 6:46 AM, Alison Harrill <AHarrill@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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