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cde.error.models in batch #62

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ghost opened this issue Mar 3, 2018 · 2 comments

ghost commented Mar 3, 2018

Do you think in scde.error.models you should also take batch effect into consideration?

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JEFworks commented Mar 5, 2018 via email

Yes, if you have batch information, you can provide that into the groups parameter so that error-modeling is done in a batch-specific manner. Jean Fan, PhD Bioinformatics and Integrative Genomics NCI F99/K00 Post-Doctoral Fellow Zhuang Lab | Harvard University 12 Oxford St, Naito 031, Cambridge, MA 02138 web: jef.works<http://jefworks.com/> On Mar 3, 2018, at 8:52 AM, Poorya Parvizi <[email protected]<mailto:[email protected]>> wrote: Do you think in scde.error.models you should also take batch effect into consideration? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hms-2Ddbmi_scde_issues_62&d=DwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=2gb0vmLv11Vi98WTAqlCXyDkhi11d9lKeGWDXEU-qNw&m=r_RQR55RzqvOlTCizv3EYm_jzWFnD56Asxssx9GiqjA&s=sBBq7SlVrB0tL5bE7-dk4kgl1RVuw-ByITcBzr3cU1k&e=>, or mute the thread<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AIj2SG3R6xRV7CNQ-2DUL8kwcGIGdc-5FVc6ks5taqAGgaJpZM4Sa7Nl&d=DwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=2gb0vmLv11Vi98WTAqlCXyDkhi11d9lKeGWDXEU-qNw&m=r_RQR55RzqvOlTCizv3EYm_jzWFnD56Asxssx9GiqjA&s=t2SoIir5CTeO9HU-57Bmkgqd9ClNm7X2289fLhwpwSA&e=>.

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ghost commented Mar 5, 2018 •

edited by ghost

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But the problem is, my single cells have two conditions which both exist in different batches.
Do you mean in this case I should have 4 groups?

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