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zfyuan / EpiProfile2.0_Family

EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data
GNU General Public License v3.0
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The specific protocol for EpiProfile software installation and usage #1

Open wuhao4850103 opened 5 years ago

wuhao4850103 commented 5 years ago

I have tried to download the EpiProfile software on the website for several times in order to identify and make quantification of histone modification during experiment, but failed every time. Hence, I want to make aquisition of the method for EpiProfile software download, so as to make analysis of histone modification on my own. Thank you very much!

zfyuan commented 5 years ago

Please follow the instructions below for the updated program usage. Thanks.

EpiProfile resources.pdf

clin888 commented 4 years ago

please assist these errors... (I used EpiProfile2.1_1Basic) Thank you so much..

LC-MS_Liver_rep1 LC-MS_Liver_rep2 LC-MS_Liver_rep3

Error using horzcat Dimensions of arrays being concatenated are not consistent.

Error in get_nDAmode (line 60) cur_ix = [0 cur_ix cycle_len];%#ok

Error in EpiProfile_test (line 79) [nDAmodes,windows] = get_nDAmode(raw_path,raw_names,startmz);

zfyuan commented 4 years ago

Hi,

Thanks for your test. Could you please share a link for me to download these three RAW files?

Best, Zuofei

On Sun, Sep 27, 2020 at 10:54 PM clin888 notifications@github.com wrote:

please assist these errors... (I used EpiProfile2.1_1Basic) Thank you so much..

LC-MS_Liver_rep1 LC-MS_Liver_rep2 LC-MS_Liver_rep3

Error using horzcat Dimensions of arrays being concatenated are not consistent.

Error in get_nDAmode (line 60) cur_ix = [0 cur_ix cycle_len];%#ok

Error in EpiProfile_test (line 79) [nDAmodes,windows] = get_nDAmode(raw_path,raw_names,startmz);

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/zfyuan/EpiProfile2.0_Family/issues/1#issuecomment-699755061, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIYLD5QLS3HUI6AKTSWXWVDSIACH7ANCNFSM4GJ4TMRA .

clin888 commented 4 years ago

Hi Zuo-Fei,

I appreciate your quick response...

Here is the URL for the data (18 raw files) https://chorusproject.org/pages/dashboard.html#/search/1546/projects/1546/experiments/3356/files?page=1&items=25&sortingField=uploadDate&asc=false

In case, you have a problem downloading this. attached is the paper. https://genome.cshlp.org/content/29/6/978.long

[cid:49aff953-b9fa-437c-859f-6f27bc8e0e7e]

Thank you so much,

Chenwei

From: Zuo-Fei Yuan notifications@github.com Sent: Monday, September 28, 2020 7:09 PM To: zfyuan/EpiProfile2.0_Family EpiProfile2.0_Family@noreply.github.com Cc: Lin PhD, ChenWei clin@fredhutch.org; Comment comment@noreply.github.com Subject: Re: [zfyuan/EpiProfile2.0_Family] The specific protocol for EpiProfile software installation and usage (#1)

Hi,

Thanks for your test. Could you please share a link for me to download these three RAW files?

Best, Zuofei

On Sun, Sep 27, 2020 at 10:54 PM clin888 notifications@github.com wrote:

please assist these errors... (I used EpiProfile2.1_1Basic) Thank you so much..

LC-MS_Liver_rep1 LC-MS_Liver_rep2 LC-MS_Liver_rep3

Error using horzcat Dimensions of arrays being concatenated are not consistent.

Error in get_nDAmode (line 60) cur_ix = [0 cur_ix cycle_len];%#ok

Error in EpiProfile_test (line 79) [nDAmodes,windows] = get_nDAmode(raw_path,raw_names,startmz);

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/zfyuan/EpiProfile2.0_Family/issues/1#issuecomment-699755061https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zfyuan_EpiProfile2.0-5FFamily_issues_1-23issuecomment-2D699755061-253E&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=OOfS3mU35Sy6z1x4H_JhwYQk8MtXGYWXf_vUARf7vQk&s=JwHheDzFrPmKdgn5fF2VnsGFErPkEXAyxLH0TEKgB2A&e=, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIYLD5QLS3HUI6AKTSWXWVDSIACH7ANCNFSM4GJ4TMRAhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AIYLD5QLS3HUI6AKTSWXWVDSIACH7ANCNFSM4GJ4TMRA-253E&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=OOfS3mU35Sy6z1x4H_JhwYQk8MtXGYWXf_vUARf7vQk&s=3ZIFpJL6eBh6a4_Me_eTK_4T7nGc1N25EhzQS_p9YGw&e= .

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zfyuan commented 4 years ago

Thanks for the link. I will test the data these days.

Best, Zuo-Fei

On Tue, Sep 29, 2020 at 12:27 AM clin888 notifications@github.com wrote:

Hi Zuo-Fei,

I appreciate your quick response...

Here is the URL for the data (18 raw files)

https://chorusproject.org/pages/dashboard.html#/search/1546/projects/1546/experiments/3356/files?page=1&items=25&sortingField=uploadDate&asc=false

In case, you have a problem downloading this. attached is the paper. https://genome.cshlp.org/content/29/6/978.long

[cid:49aff953-b9fa-437c-859f-6f27bc8e0e7e]

Thank you so much,

Chenwei

From: Zuo-Fei Yuan notifications@github.com Sent: Monday, September 28, 2020 7:09 PM To: zfyuan/EpiProfile2.0_Family EpiProfile2.0_Family@noreply.github.com Cc: Lin PhD, ChenWei clin@fredhutch.org; Comment < comment@noreply.github.com> Subject: Re: [zfyuan/EpiProfile2.0_Family] The specific protocol for EpiProfile software installation and usage (#1)

Hi,

Thanks for your test. Could you please share a link for me to download these three RAW files?

Best, Zuofei

On Sun, Sep 27, 2020 at 10:54 PM clin888 notifications@github.com wrote:

please assist these errors... (I used EpiProfile2.1_1Basic) Thank you so much..

LC-MS_Liver_rep1 LC-MS_Liver_rep2 LC-MS_Liver_rep3

Error using horzcat Dimensions of arrays being concatenated are not consistent.

Error in get_nDAmode (line 60) cur_ix = [0 cur_ix cycle_len];%#ok

Error in EpiProfile_test (line 79) [nDAmodes,windows] = get_nDAmode(raw_path,raw_names,startmz);

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/zfyuan/EpiProfile2.0_Family/issues/1#issuecomment-699755061 < https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zfyuan_EpiProfile2.0-5FFamily_issues_1-23issuecomment-2D699755061-253E&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=OOfS3mU35Sy6z1x4H_JhwYQk8MtXGYWXf_vUARf7vQk&s=JwHheDzFrPmKdgn5fF2VnsGFErPkEXAyxLH0TEKgB2A&e= , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AIYLD5QLS3HUI6AKTSWXWVDSIACH7ANCNFSM4GJ4TMRA < https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AIYLD5QLS3HUI6AKTSWXWVDSIACH7ANCNFSM4GJ4TMRA-253E&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=OOfS3mU35Sy6z1x4H_JhwYQk8MtXGYWXf_vUARf7vQk&s=3ZIFpJL6eBh6a4_Me_eTK_4T7nGc1N25EhzQS_p9YGw&e=

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zfyuan commented 4 years ago

I see what is the issue.

DI-MS_Liver_Wideisolation_rep1 DI-MS_Liver_Wideisolation_rep2 DI-MS_Liver_Wideisolation_rep3 LC-MS_Brain_rep1 LC-MS_Brain_rep2 LC-MS_Brain_rep3 LC-MS_Liver_rep1 LC-MS_Liver_rep2 LC-MS_Liver_rep3 Error using horzcat Dimensions of arrays being concatenated are not consistent.

The files starting with 'DI' are very small. The files starting with 'LC' are very big. EpiProfile2.1_1Basic can only process the 'LC' files. EpiProfileLite ( https://github.com/zfyuan/EpiProfileLite) can process the 'DI' files. So please separate those files first.

Best, Zuo-Fei

On Tue, Sep 29, 2020 at 12:27 AM clin888 notifications@github.com wrote:

Hi Zuo-Fei,

I appreciate your quick response...

Here is the URL for the data (18 raw files)

https://chorusproject.org/pages/dashboard.html#/search/1546/projects/1546/experiments/3356/files?page=1&items=25&sortingField=uploadDate&asc=false

In case, you have a problem downloading this. attached is the paper. https://genome.cshlp.org/content/29/6/978.long

[cid:49aff953-b9fa-437c-859f-6f27bc8e0e7e]

Thank you so much,

Chenwei

From: Zuo-Fei Yuan notifications@github.com Sent: Monday, September 28, 2020 7:09 PM To: zfyuan/EpiProfile2.0_Family EpiProfile2.0_Family@noreply.github.com Cc: Lin PhD, ChenWei clin@fredhutch.org; Comment < comment@noreply.github.com> Subject: Re: [zfyuan/EpiProfile2.0_Family] The specific protocol for EpiProfile software installation and usage (#1)

Hi,

Thanks for your test. Could you please share a link for me to download these three RAW files?

Best, Zuofei

On Sun, Sep 27, 2020 at 10:54 PM clin888 notifications@github.com wrote:

please assist these errors... (I used EpiProfile2.1_1Basic) Thank you so much..

LC-MS_Liver_rep1 LC-MS_Liver_rep2 LC-MS_Liver_rep3

Error using horzcat Dimensions of arrays being concatenated are not consistent.

Error in get_nDAmode (line 60) cur_ix = [0 cur_ix cycle_len];%#ok

Error in EpiProfile_test (line 79) [nDAmodes,windows] = get_nDAmode(raw_path,raw_names,startmz);

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/zfyuan/EpiProfile2.0_Family/issues/1#issuecomment-699755061 < https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zfyuan_EpiProfile2.0-5FFamily_issues_1-23issuecomment-2D699755061-253E&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=OOfS3mU35Sy6z1x4H_JhwYQk8MtXGYWXf_vUARf7vQk&s=JwHheDzFrPmKdgn5fF2VnsGFErPkEXAyxLH0TEKgB2A&e= , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AIYLD5QLS3HUI6AKTSWXWVDSIACH7ANCNFSM4GJ4TMRA < https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AIYLD5QLS3HUI6AKTSWXWVDSIACH7ANCNFSM4GJ4TMRA-253E&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=OOfS3mU35Sy6z1x4H_JhwYQk8MtXGYWXf_vUARf7vQk&s=3ZIFpJL6eBh6a4_Me_eTK_4T7nGc1N25EhzQS_p9YGw&e=

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clin888 commented 4 years ago

Hi Zuo-Fei,

I really appreciate your hard working.. Thank you for your help and efforts, Happy moon festival..

Chenwei

From: Zuo-Fei Yuan notifications@github.com Sent: Thursday, October 1, 2020 8:40 PM To: zfyuan/EpiProfile2.0_Family EpiProfile2.0_Family@noreply.github.com Cc: Lin PhD, ChenWei clin@fredhutch.org; Comment comment@noreply.github.com Subject: Re: [zfyuan/EpiProfile2.0_Family] The specific protocol for EpiProfile software installation and usage (#1)

I see what is the issue.

DI-MS_Liver_Wideisolation_rep1 DI-MS_Liver_Wideisolation_rep2 DI-MS_Liver_Wideisolation_rep3 LC-MS_Brain_rep1 LC-MS_Brain_rep2 LC-MS_Brain_rep3 LC-MS_Liver_rep1 LC-MS_Liver_rep2 LC-MS_Liver_rep3 Error using horzcat Dimensions of arrays being concatenated are not consistent.

The files starting with 'DI' are very small. The files starting with 'LC' are very big. EpiProfile2.1_1Basic can only process the 'LC' files. EpiProfileLite ( https://github.com/zfyuan/EpiProfileLitehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zfyuan_EpiProfileLite&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=Umlt-lqnEkwAVYjTVBEnmRQpEssZ2ZRcRLUzBnjbVyo&s=xn_Y2y7epOkzPOQtHKb5v1aY30imIR8omnHuxZoLTO8&e=) can process the 'DI' files. So please separate those files first.

Best, Zuo-Fei

On Tue, Sep 29, 2020 at 12:27 AM clin888 notifications@github.com wrote:

Hi Zuo-Fei,

I appreciate your quick response...

Here is the URL for the data (18 raw files)

https://chorusproject.org/pages/dashboard.html#/search/1546/projects/1546/experiments/3356/files?page=1&items=25&sortingField=uploadDate&asc=falsehttps://urldefense.proofpoint.com/v2/url?u=https-3A__chorusproject.org_pages_dashboard.html-23_search_1546_projects_1546_experiments_3356_files-3Fpage-3D1-26items-3D25-26sortingField-3DuploadDate-26asc-3Dfalse&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=Umlt-lqnEkwAVYjTVBEnmRQpEssZ2ZRcRLUzBnjbVyo&s=Ybs0HFp6bBSG6xJQnJ_5G4-PXN8fzo5hLa0Q1XfHmv4&e=

In case, you have a problem downloading this. attached is the paper. https://genome.cshlp.org/content/29/6/978.longhttps://urldefense.proofpoint.com/v2/url?u=https-3A__genome.cshlp.org_content_29_6_978.long&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=Umlt-lqnEkwAVYjTVBEnmRQpEssZ2ZRcRLUzBnjbVyo&s=2LZe04fTMfhYugj4b8bqbTDMOPPCuuGgp2OQpsDADRE&e=

[cid:49aff953-b9fa-437c-859f-6f27bc8e0e7e]

Thank you so much,

Chenwei

From: Zuo-Fei Yuan notifications@github.com Sent: Monday, September 28, 2020 7:09 PM To: zfyuan/EpiProfile2.0_Family EpiProfile2.0_Family@noreply.github.com Cc: Lin PhD, ChenWei clin@fredhutch.org; Comment < comment@noreply.github.com> Subject: Re: [zfyuan/EpiProfile2.0_Family] The specific protocol for EpiProfile software installation and usage (#1)

Hi,

Thanks for your test. Could you please share a link for me to download these three RAW files?

Best, Zuofei

On Sun, Sep 27, 2020 at 10:54 PM clin888 notifications@github.com wrote:

please assist these errors... (I used EpiProfile2.1_1Basic) Thank you so much..

LC-MS_Liver_rep1 LC-MS_Liver_rep2 LC-MS_Liver_rep3

Error using horzcat Dimensions of arrays being concatenated are not consistent.

Error in get_nDAmode (line 60) cur_ix = [0 cur_ix cycle_len];%#ok

Error in EpiProfile_test (line 79) [nDAmodes,windows] = get_nDAmode(raw_path,raw_names,startmz);

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/zfyuan/EpiProfile2.0_Family/issues/1#issuecomment-699755061https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zfyuan_EpiProfile2.0-5FFamily_issues_1-23issuecomment-2D699755061&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=Umlt-lqnEkwAVYjTVBEnmRQpEssZ2ZRcRLUzBnjbVyo&s=ArnejMRwiFYf2x43vqS2uw6e-tfLpODoztEEShE59VI&e= < https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zfyuan_EpiProfile2.0-5FFamily_issues_1-23issuecomment-2D699755061-253E&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=OOfS3mU35Sy6z1x4H_JhwYQk8MtXGYWXf_vUARf7vQk&s=JwHheDzFrPmKdgn5fF2VnsGFErPkEXAyxLH0TEKgB2A&e= , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AIYLD5QLS3HUI6AKTSWXWVDSIACH7ANCNFSM4GJ4TMRAhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AIYLD5QLS3HUI6AKTSWXWVDSIACH7ANCNFSM4GJ4TMRA&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=Umlt-lqnEkwAVYjTVBEnmRQpEssZ2ZRcRLUzBnjbVyo&s=MYEy0q-EO7cSfFKy2W1Da6_pdTGBvYNYr5OgVomxqhs&e= < https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AIYLD5QLS3HUI6AKTSWXWVDSIACH7ANCNFSM4GJ4TMRA-253E&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=OOfS3mU35Sy6z1x4H_JhwYQk8MtXGYWXf_vUARf7vQk&s=3ZIFpJL6eBh6a4_Me_eTK_4T7nGc1N25EhzQS_p9YGw&e=

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