{"id":14977274,"url":"https://github.com/pwilmart/irs_normalization","last_synced_at":"2025-10-28T03:31:02.207Z","repository":{"id":94498928,"uuid":"119600267","full_name":"pwilmart/IRS_normalization","owner":"pwilmart","description":"An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.","archived":false,"fork":false,"pushed_at":"2019-08-06T14:05:38.000Z","size":33655,"stargazers_count":15,"open_issues_count":1,"forks_count":9,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-02-01T10:41:37.319Z","etag":null,"topics":["ipynb","irs-normalization","jupyter-notebook","mass-spectrometry","normalization","proteomics","proteomics-data","r","tmt"],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pwilmart.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-01-30T22:04:49.000Z","updated_at":"2024-03-05T16:41:17.000Z","dependencies_parsed_at":"2023-03-31T16:02:39.853Z","dependency_job_id":null,"html_url":"https://github.com/pwilmart/IRS_normalization","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pwilmart%2FIRS_normalization","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pwilmart%2FIRS_normalization/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pwilmart%2FIRS_normalization/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pwilmart%2FIRS_normalization/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pwilmart","download_url":"https://codeload.github.com/pwilmart/IRS_normalization/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":238590593,"owners_count":19497351,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["ipynb","irs-normalization","jupyter-notebook","mass-spectrometry","normalization","proteomics","proteomics-data","r","tmt"],"created_at":"2024-09-24T13:55:23.498Z","updated_at":"2025-10-28T03:30:52.197Z","avatar_url":"https://github.com/pwilmart.png","language":"Jupyter Notebook","readme":"# IRS_normalization\nAn exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments. Also, examples of how IRS-normalized data affects statistical testing, and how to avoid using ratios in the analyses. \n\nThe IRS method was first described in this publication:\n\u003e Plubell, D.L., Wilmarth, P.A., Zhao, Y., Fenton, A.M., Minnier, J., Reddy, A.P., Klimek, J., Yang, X., David, L.L. and Pamir, N., 2017. Extended multiplexing of tandem mass tags (TMT) labeling reveals age and high fat diet specific proteome changes in mouse epididymal adipose tissue. Molecular \u0026 Cellular Proteomics, 16(5), pp.873-890.\n\nThe analysis is of a mouse lens development time course (6 points 3 days apart from E15 to P9) where three replicates of the time points were done in 3 separate TMT labelings. The lens is a unique system that has been studied for many years and the prior knowledge can be used to guide some analysis steps. The data is from this publication:\n\u003e Khan, S.Y., Ali, M., Kabir, F., Renuse, S., Na, C.H., Talbot, C.C., Hackett, S.F. and Riazuddin, S.A., 2018. Proteome Profiling of Developing Murine Lens Through Mass Spectrometry. Investigative Ophthalmology \u0026 Visual Science, 59(1), pp.100-107.\n\n## Contents:\nFour [jupyter notebook](http://jupyter.org) files (R kernel). If you click on the notebook files (*.ipynb extensions), they will render and display in your bowser. Please be patient as they can take a minute to render.\n* understanding_IRS.ipynb is Part 1 (normalizations)\n* statistical_testing.ipynb is Part 2 (edgeR testing)\n* statistical_testing_ratios.ipynb is Part 3 (taking ratios and using limma)\n* statistical_testing_take2.ipynb is Part 4 (testing P0 vs P3)\n\nData from Kahn, et al.:\n* iovs_58-13-55-s01.csv\n\nSample information for design matrix:\n* design.csv\n\nSaved results from the statisticl testing:\n* final_part3.csv (and final_part3.xlsx)\n\nAdded HTML renderings of the notebooks for those who just want to see the analysis steps and figures (these may load faster):\n* [understanding_IRS.html](https://pwilmart.github.io/IRS_normalization/understanding_IRS.html) is Part 1 (needs the png file)\n* irs_diagram.png is an image for the understanding_IRS.html script\n* [statistical_testing.html](https://pwilmart.github.io/IRS_normalization/statistical_testing.html) is Part 2\n* [statistical_testing_ratios.html](https://pwilmart.github.io/IRS_normalization/statistical_testing_ratios.html) is Part 3\n* [statistical_testing_take2.html](https://pwilmart.github.io/IRS_normalization/statistical_testing_take2.html) is Part 4\n\nAdded R scripts extracted from the notebooks. These can be used in RStudio or modified for your own analyses.\n\n## Other repositories that may be of interest:\n* [TMT data analysis examples](https://github.com/pwilmart/TMT_analysis_examples.git)\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpwilmart%2Firs_normalization","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpwilmart%2Firs_normalization","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpwilmart%2Firs_normalization/lists"}