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Messages - kcurran

1
XCMS Online / File check and TICs failed
Hi there,

What is your best advice for dealing with this error message: "File check and TICs failed" when doing a pairwise job using XCMS Online?  This happened for me on this job: pair_2016-03-24_10:02

Thanks,
Katherine.
2
XCMS Online / centwave for Centroided data
Hi there,

This seems like a stupid question but I assume that I need to use the centwave algorithm for centroided MS data in XCMS online?  My data is GCMS data.

Thanks!
Katherine.
3
XCMS Online / Re: Problem with pairwise jobs
Hi yes - XCMS online.

I have looked into this a bit more.  It is working fine when I am at home but not in my university (University College London) even when using the same laptop.
This was not a problem previously, has anything changed recently that would cause my university to block the page?

I have contacted our university IT support but they have been unable to help.

Best,
Katherine.
4
XCMS Online / Problem with pairwise jobs
Hi there,
I'm using XCMS on a new computer and have problems creating a pairwise job.  If I click on the menu option, nothing appears, just a blank screen.  I have tried in both Internet Explorer and Firefox.  My computer is a Dell XPS12 using Windows 8.
Help!
Katherine.
5
XCMS Online / Re: FILE_READ_ERROR
Hi Ralf,

Thanks for your help.  I've never used anything other than the GUI version of msconvert before .  I have the file for the non-GUI version on my computer but am having difficulties opening it, when I try to open it, a window opens, it scrolls through a load of command lines and then shuts again.  Do you have any suggestions for this one?  I'm afraid I've never really used command-line type software at all!

Katherine.
7
XCMS Online / FILE_READ_ERROR
Hi there,

I'm having a problem with 3 files in one of my datasets.  I get an error message after submitting the job: FILE_READ_ERROR and then when I look through my datasets, 3 of the files have this message (or similar):

Error in xcmsRaw(file, profstep = 0) : Time for scan 7998 (3600) greater than scan 7999 (0.402).

I tried re-uploading the files, and then tried re-converting them from .raw to .mzXML and re-uploading again but I get the same message with the same 3 files.  All of my other files are fine, and are all from the same instrument (Perkin Elmer), same type of samples.

For my chromatograms, scans with values around 7998 are right at the end, and I'd be happy to remove these scans if there's a problem with them.  Is it possible to do this?  Or is there any other way to work around this?

This is job no. 1002815, I'm using Firefox and Windows 7.

Thanks,
Katherine.
8
XCMS Online / Re: Invalid checksum
Hi Duane,

Thanks for your reply.  I re-uploaded the problem files and re-submitted the job.  Almost all of the files have been fine, which is great.  However, I've an error message for 3 of them:

Error in xcmsRaw(file, profstep = 0) : Time for scan 7998 (3600) greater than scan 7999 (0.402)

Is there anything I can do about this?  It's only 3 samples out of over 200, but 2 of them in particular are quite important ones, I'd rather not just delete them.

Best,
Katherine.
9
XCMS Online / Invalid checksum
Hi there,

I am having a problem after I submit my job, I get an error message that says MD5_FILE_CHECK_FAILED.

Looking at the files, it was the first file in the first dataset that caused the problem, the error message is "Invalid checksum".  I tried removing this file, but it I got the same problem with the next file too.

My job number is 1002782.

I have converted .raw files to .mzXML files and have been able to upload and process similar files previously.

Any suggestions welcome!

Katherine.
10
XCMS Online / Re: Storage Quota problem?
Dear Duane,

Thanks for your advice.  I had already removed all other datasets and results, so there's no room for extra space.  I wondered if there was any way of making my file sizes smaller?  Currently I have 2 datasets, each with about 100 GC/MS chromatograms, and they're both a little over 1GB each.  Do you know of any conversions I can do to get smaller file sizes?  Or is 100 files an unusually large dataset?

I've put in a request for extra storage through the contact page, and have also completed the user survey.  I also wanted to ask about your other suggestion, do I need to pay for XCMS through Bioconductor?

Best,
Katherine.
11
XCMS Online / Storage Quota problem?
Hi there,

I'm having problems submitting a job.  When I press Submit, I get an error message, "Please correct errors or contact system administrator to proceed".

I think the problem might be that my datasets are quite big - around 100 files each.  I am over my storage quota, and have a message to say that Uploads are disabled.  Does this mean that I'm also unable to submit a job?  Is there anything I can do about this?

I'm using Firefox 12.0 on Windows 7.  My files are .raw GC/MS files from a Perkin Elmer instrument, which I've converted to .mzXML files.  I've run successful jobs in the past using these file types and the same parameters.  Job number is 1002395, although it hasn't actually run.

Any advice welcome!
K.