heatmap.2 Z-score vs logFC
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Neel Aluru ▴ 460
@neel-aluru-3760
Last seen 7.3 years ago
United States
Hello Bioc Users, I am having a hard time understanding why heatmap.2 uses row (or column) Z-score instead of directly plotting logFC values? Based on the formula for calculating Z-score, I understand that it is used for scaling or smoothing. But, isn't it the same when using logFC. Please correct if I am wrong. I really appreciate if anyone can give me a clear explanation. Sorry for asking a silly question. I -- Neel Aluru Visiting Investigator Biology Department Woods Hole Oceanographic Institution 45 Woods Hole Road Woods Hole 02543 Massachusetts USA
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@ochsner-scott-a-4334
Last seen 9.6 years ago
Neel, You just need to do a little more digging within the help for heatmap.2. See ?heatmap.2 and read the description of just what applying scale to rows actually does to your values. Scott Ochsner Baylor College of Medicine One Baylor Plaza Houston, TX 77030 > -----Original Message----- > From: bioconductor-bounces at r-project.org [mailto:bioconductor- bounces at r- > project.org] On Behalf Of Neel Aluru > Sent: Tuesday, October 18, 2011 10:33 AM > To: bioconductor at r-project.org > Subject: [BioC] heatmap.2 Z-score vs logFC > > Hello Bioc Users, > > I am having a hard time understanding why heatmap.2 uses row (or column) Z- > score instead of directly plotting logFC values? Based on the formula for > calculating Z-score, I understand that it is used for scaling or smoothing. But, > isn't it the same when using logFC. Please correct if I am wrong. I really > appreciate if anyone can give me a clear explanation. > > Sorry for asking a silly question. I > > -- > Neel Aluru > Visiting Investigator > Biology Department > Woods Hole Oceanographic Institution > 45 Woods Hole Road > Woods Hole 02543 > Massachusetts > USA > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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@sean-davis-490
Last seen 12 weeks ago
United States
Hi, Neel. Some rows have larger logFC than others. Without scaling, those rows will be brighter than the rows that have smaller logFC. Scaling the rows (columns) makes the rows (columns) have similar variation so that even rows that have smaller logFC still have visible changes when plotted. If most of your rows (columns) have similar variation, then scaling will not make much difference. Sean On Tue, Oct 18, 2011 at 11:33 AM, Neel Aluru <naluru at="" whoi.edu=""> wrote: > Hello Bioc Users, > > I am having a hard time understanding why heatmap.2 uses row (or column) > Z-score instead of directly plotting logFC values? ?Based on the formula for > calculating Z-score, I understand that it is used for scaling or smoothing. > But, isn't it the same when using logFC. Please correct if I am wrong. I > really appreciate if anyone can give me a clear explanation. > > Sorry for asking a silly question. I > > -- > Neel Aluru > Visiting Investigator > Biology Department > Woods Hole Oceanographic Institution > 45 Woods Hole Road > Woods Hole 02543 > Massachusetts > USA > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Thank you so much for clarifying. It makes total sense. Neel On 10/18/11 11:44 AM, Sean Davis wrote: > Hi, Neel. > > Some rows have larger logFC than others. Without scaling, those rows > will be brighter than the rows that have smaller logFC. Scaling the > rows (columns) makes the rows (columns) have similar variation so that > even rows that have smaller logFC still have visible changes when > plotted. If most of your rows (columns) have similar variation, then > scaling will not make much difference. > > Sean > > On Tue, Oct 18, 2011 at 11:33 AM, Neel Aluru<naluru at="" whoi.edu=""> wrote: >> Hello Bioc Users, >> >> I am having a hard time understanding why heatmap.2 uses row (or column) >> Z-score instead of directly plotting logFC values? Based on the formula for >> calculating Z-score, I understand that it is used for scaling or smoothing. >> But, isn't it the same when using logFC. Please correct if I am wrong. I >> really appreciate if anyone can give me a clear explanation. >> >> Sorry for asking a silly question. I >> >> -- >> Neel Aluru >> Visiting Investigator >> Biology Department >> Woods Hole Oceanographic Institution >> 45 Woods Hole Road >> Woods Hole 02543 >> Massachusetts >> USA >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> -- Neel Aluru Visiting Investigator Biology Department Woods Hole Oceanographic Institution 45 Woods Hole Road Woods Hole 02543 Massachusetts USA
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