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compomics / reporter

Protein quantification based on reporter ions
http://compomics.github.io/projects/reporter.html
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Reporter error #1

Closed ghost closed 8 years ago

ghost commented 8 years ago

Hi,

I tried to use reporter for my iTRAQ8 experiment. I tried to open the Peptideshaker results with reporter. But reporter is constantly giving this error message. The number of clusters cannot be bigger than the number of samples: #clusters:18, #samples:14. It also says please contact the developers if this persists.

I appreciate your help

Thanks

Nijat

mvaudel commented 8 years ago

Dear Nijat,

Thank you for reporting this issue - the first on the Reporter Github!

Would it be possible for you to make the PeptideShaker project available to us? Please export it as zip file from PeptideShaker using the Export -> PeptideShaker Project As... -> Zip menu so that I can open it on my side as well.

Many thanks and apologies for the inconvenience,

Marc

ghost commented 8 years ago

Hi Marc,

Thank you for the fast response! The file is big, so I am sharing a link to the file through google drive here: https://drive.google.com/open?id=0BwzoAa1-C0ifcTk4U00tVHhCMU0 Hope you can open it.

Thanks again

Nijat

mvaudel commented 8 years ago

Hi again and thank you for the PeptideShaker file. Can you also attach the mgfs and fasta files? Alternatively, export the PeptideShaker project as zip file from PeptideShaker using the Export -> PeptideShaker Project As... -> Zip menu.

ghost commented 8 years ago

HI Marc,

I have uploaded the mgf.zip file to the same link. Hope this helps.

https://drive.google.com/open?id=0BwzoAa1-C0ifSnZEZEUya3BfNmc

Sorry for not getting back to you on time.

Thanks

Nijat

On Wed, Aug 3, 2016 at 9:58 AM, Marc Vaudel notifications@github.com wrote:

Hi again and thank you for the PeptideShaker file. Can you also attach the mgfs and fasta files? Alternatively, export the PeptideShaker project as zip file from PeptideShaker using the Export -> PeptideShaker Project As... -> Zip menu.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/reporter/issues/1#issuecomment-237282541, or mute the thread https://github.com/notifications/unsubscribe-auth/ALqg-4TKRrt7v5sWFHC7ENphURQOINwEks5qcMidgaJpZM4JK6f5 .

Nijiati Abulizi BSc, MSc student

Biochemistry and Molecular Biology, IKBSAS

The University of British Columbia | Okanagan Campus

ASC 365, 3187 University Way

Kelowna, BC V1V-1V7, Canada

(778)2145086| nijiati.abulizi@ubc.ca

hbarsnes commented 8 years ago

Hi Nijat,

Thanks for the files. Now we're just missing your FASTA file before we can try to load the data in our side.

Note that the easiest way to share a PeptideShaker project is to use Export > PeptideShaker Project As > Zip File. This generate a single zip file with all the required files for opening the project on a different computer.

Best regards, Harald

ghost commented 8 years ago

Hi Harald,

I just added the fasta file to the drive. Please let me know if you need anything else.

Thanks

Nijat

On Wed, Aug 31, 2016 at 3:38 PM, Harald Barsnes notifications@github.com wrote:

Hi Nijat,

Thanks for the files. Now we're just missing your FASTA file before we can try to load the data in our side.

Note that the easiest way to share a PeptideShaker project is to use *Export

PeptideShaker Project As > Zip File*. This generate a single zip file with all the required files for opening the project on a different computer.

Best regards, Harald

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/reporter/issues/1#issuecomment-243924297, or mute the thread https://github.com/notifications/unsubscribe-auth/ALqg-xRXeGYheOj9ZocyxGhfWWXY6gNPks5qlgKAgaJpZM4JK6f5 .

Nijiati Abulizi BSc, MSc student

Biochemistry and Molecular Biology, IKBSAS

The University of British Columbia | Okanagan Campus

ASC 365, 3187 University Way

Kelowna, BC V1V-1V7, Canada

(778)2145086| nijiati.abulizi@ubc.ca

hbarsnes commented 8 years ago

Hi Nijat,

I think I need the link to the FASTA file? At least I cannot find a way of getting to it from the links above?

Best regards, Harald

ghost commented 8 years ago

Hi Harald,

Here is the link https://drive.google.com/open?id=0BwzoAa1-C0ifQjVZOFRISm9VSFU

I appreciate your help.

Thanks

On Wed, Aug 31, 2016 at 4:12 PM, Nijiati Abulizi nijiati.abulizi@gmail.com wrote:

Hi Harald,

I just added the fasta file to the drive. Please let me know if you need anything else.

Thanks

Nijat

On Wed, Aug 31, 2016 at 3:38 PM, Harald Barsnes notifications@github.com wrote:

Hi Nijat,

Thanks for the files. Now we're just missing your FASTA file before we can try to load the data in our side.

Note that the easiest way to share a PeptideShaker project is to use *Export

PeptideShaker Project As > Zip File*. This generate a single zip file with all the required files for opening the project on a different computer.

Best regards, Harald

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/reporter/issues/1#issuecomment-243924297, or mute the thread https://github.com/notifications/unsubscribe-auth/ALqg-xRXeGYheOj9ZocyxGhfWWXY6gNPks5qlgKAgaJpZM4JK6f5 .

Nijiati Abulizi BSc, MSc student

Biochemistry and Molecular Biology, IKBSAS

The University of British Columbia | Okanagan Campus

ASC 365, 3187 University Way

Kelowna, BC V1V-1V7, Canada

(778)2145086| nijiati.abulizi@ubc.ca

Nijiati Abulizi BSc, MSc student

Biochemistry and Molecular Biology, IKBSAS

The University of British Columbia | Okanagan Campus

ASC 365, 3187 University Way

Kelowna, BC V1V-1V7, Canada

(778)2145086| nijiati.abulizi@ubc.ca

hbarsnes commented 8 years ago

Hi Nijat,

Thanks for the FASTA file. However, it does not seem to be the correct one? At least I'm not able to open the project using this file.

Please use Export > PeptideShaker Project As > Zip File and share the resulting zip file instead?

Best regards, Harald

ghost commented 8 years ago

Hi Harald,

I have created the ZIP file from peptide shaker and put it together with the other files. Hope this opens on your end.

https://drive.google.com/open?id=0BwzoAa1-C0ifN21naVB2VXhSTlE

Thank you

Nijat

On Thu, Sep 1, 2016 at 3:19 PM, Harald Barsnes notifications@github.com wrote:

Hi Nijat,

Thanks for the FASTA file. However, it does not seem to be the correct one? At least I'm not able to open the project using this file.

Please use Export > PeptideShaker Project As > Zip File and share the resulting zip file instead?

Best regards, Harald

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/reporter/issues/1#issuecomment-244230272, or mute the thread https://github.com/notifications/unsubscribe-auth/ALqg-xntUQooAhidO2jz1chcKttgkf7oks5ql098gaJpZM4JK6f5 .

Nijiati Abulizi BSc, MSc student

Biochemistry and Molecular Biology, IKBSAS

The University of British Columbia | Okanagan Campus

ASC 365, 3187 University Way

Kelowna, BC V1V-1V7, Canada

(778)2145086| nijiati.abulizi@ubc.ca

hbarsnes commented 8 years ago

Hi Nijat,

The problems seems to be that you have very few validated proteins in your PeptideShaker dataset. In fact only 7 proteins are validated, all listed as doubtful. The default number of clusters in Reporter is 18, and it's a bit difficult to separate 7 proteins into 18 clusters. We'll remove this limitation in the next release of Reporter, but I would recommend that you look into your search settings to see if there are any parameters you could optimize to improve your results and increase the number of validated proteins.

I will let you know when the new Reporter version becomes available.

Best regards, Harald

hbarsnes commented 8 years ago

Hi Nijat,

We've just released Reporter v0.5.4 which should allow you to open your dataset. If this is not the case please let us know and we'll reopen the issue.

Best regards, Harald