Closed GettyScience closed 6 months ago
dariotommasini
commented
10 months ago Can you describe in more detail what exactly you want for each gene? Connectivity values are available in the object@datExpr slot of the WGCNA objects. For example, for the astrocyte combined network, you can retrieve them for each gene like this:
head(astrocyte_networks$combined@datExpr[,c("kTotal", "kWithin", "kOut", "kDiff")])I believe kWithin is kME (intramodular connectivity).
smukher2
commented
6 months ago PLEASE HELP STOP PLAGIARISM AND VILLAINOUS SCIENTISTS BRENT FOGEL (UCLA) AND DARIO TOMMASINI (now PhD student in UC Berkeley) BY NOT CITING OR USING THIS, OR THEIR OTHER CODES AND PAPERS BY THEM. INSTEAD USE AND CITE THE ORIGINAL WORKS (WITH VIDEO TUTORIAL) BY DR. STEVE HORVATH, DR. PETER LANGFELDER AND DR. JEREMY MILLER.(details below)
*For details about wrong doings by Brent Fogel including and not limited to plagiarism by Brent Fogel and Dario Tommasini please see open letter at http://tinyurl.com/bde788x2 or file 'This To Apprise You About Wrong Doings By Brent Fogel including and not limited to plagiarism by Brent Fogel and Dario Tommasini.pdf' posted at https://gitlab.com/smukher2/openletter that I also emailed to UCLA, UC Berkeley, iScience and BMC Bioinformatics reporting plagiarism by Brent Fogel and Dario Tommasini in their two papers using this multiWGCNA code https://github.com/fogellab/multiWGCNA: Tommasini D, Fox R, Ngo KJ, Hinman JD, Fogel BL. Alterations in oligodendrocyte transcriptional networks reveal region-specific vulnerabilities to neurological disease. iScience. 2023 Mar 8;26(4):106358. doi: 10.1016/j.isci.2023.106358. PMID: 36994077; PMCID: PMC10040735. Tommasini D, Fogel BL. multiWGCNA: an R package for deep mining gene co-expression networks in multi-trait expression data. BMC Bioinformatics. 2023 Mar 24;24(1):115. doi: 10.1186/s12859-023-05233-z. PMID: 36964502; PMCID: PMC10039544.
*If you need WGCNA codes for different applications with video turorial consider using the original works (with video tutorials) by Dr. Steve Horvath, Dr. Peter Langfelder and Dr. Jeremy Miller: Langfelder, P., Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9, 559 (2008). https://doi.org/10.1186/1471-2105-9-559 Miller JA, Horvath S, Geschwind DH. Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. Proc Natl Acad Sci U S A. 2010 Jul 13;107(28):12698-703. Epub 2010 Jun 25. PMID: 20616000; PMCID: PMC2906579. https://doi.org/10.1073/pnas.0914257107
Video: Dr. Steve Horvath Weighted gene co-expression network analysis https://youtu.be/rRIRMW_RRS4?si=A-ZivIzwdRVLpaLa Video: Dr. Jeremy Miller How WGCNA Can be Used to Compare and Contrast Two Networks https://youtu.be/aBD67YmCBK4?si=eW9Ybv2nIWDUjkdT Full Playlist: WGCNA https://www.youtube.com/playlist?list=PLtlynCnS_vmB2kwhfkcfxIDbsSO9uniM5 Resources: Dr. Peter Langfelder lists further resources on his website https://peterlangfelder.com/2018/11/25/wgcna-resources-on-the-web/
Best regards, Shradha Mukherjee https://gitlab.com/smukher2 https://github.com/smukher2 https://orcid.org/0000-0002-3249-2551 https://pubmed.ncbi.nlm.nih.gov/?term=Shradha+Mukherjee
Hello,
First, I wanted to say thank you for your help with previous issues. This is less of an issue and more just need some help. Is there a way that I can export information such as z-score, p-value, KME, etc., for module membership of each gene in each treatment? How can I do this in a table format?
I need to confirm the authenticity of my findings for my advisor.
Thank you,