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two questions associated with heatmap

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Weiwei Shi ★ 1.2k

@weiwei-shi-1407

Last seen 10.6 years ago

hi, there: i have 2 questions associated with heatmap in heatmap.2{gplot}, there is a bar called "raw z-score" showing the coloring legend for each pixel. Where can I find that z-score's formulae? question 2, for example, I have 5 groups and I want to label each group with a color name from "#FF0000" to "#0000FF" evenly. so basically i need a vector like this: c("#FF0000", ?, ?, ?, "#0000FF") the number of groups can be 10 or whatever. thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

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ADD COMMENT • link updated 18.6 years ago by Sean Davis 21k • written 18.6 years ago by Weiwei Shi ★ 1.2k

score 0 · Answer 1 · 2006-09-23

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Sean Davis 21k

@sean-davis-490

Last seen 9 weeks ago

United States

Weiwei Shi wrote: > hi, there: > i have 2 questions associated with heatmap > > in heatmap.2{gplot}, there is a bar called "raw z-score" showing the > coloring legend for each pixel. Where can I find that z-score's > formulae? > A Z-score is the mean of the group divided by the standard deviation. > question 2, > for example, I have 5 groups and I want to label each group with a > color name from "#FF0000" to "#0000FF" evenly. so basically i need a > vector like this: > c("#FF0000", ?, ?, ?, "#0000FF") > You could look at RColorBrewer or geneplotter for some ideas on how to do this. If you don't have a copy of the Bioconductor book, it may be a good idea to pick one up. It is quite helpful for getting started using bioconductor and gene expression data. Hope this helps. Sean

ADD COMMENT • link 18.6 years ago Sean Davis 21k

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Sean Davis wrote: > Weiwei Shi wrote: > >> hi, there: >> i have 2 questions associated with heatmap >> >> in heatmap.2{gplot}, there is a bar called "raw z-score" showing the >> coloring legend for each pixel. Where can I find that z-score's >> formulae? >> >> > A Z-score is the mean of the group divided by the standard deviation. > It's a bit late--what I meant to say is that the z-score is the ("actual value" minus the mean of the group) divided by the standard deviation. Sean

ADD REPLY • link 18.6 years ago Sean Davis 21k

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oh, i mean how it defines the group? i just want to confirm if it is based on the whole matrix? On 9/23/06, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > Sean Davis wrote: > > Weiwei Shi wrote: > > > >> hi, there: > >> i have 2 questions associated with heatmap > >> > >> in heatmap.2{gplot}, there is a bar called "raw z-score" showing the > >> coloring legend for each pixel. Where can I find that z-score's > >> formulae? > >> > >> > > A Z-score is the mean of the group divided by the standard deviation. > > > It's a bit late--what I meant to say is that the z-score is the ("actual > value" minus the mean of the group) divided by the standard deviation. > > Sean > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

ADD REPLY • link 18.6 years ago Weiwei Shi ★ 1.2k

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Weiwei Shi wrote: > oh, i mean how it defines the group? i just want to confirm if it is > based on the whole matrix? The process is typically done within each probe, not across the entire matrix, but it depends a bit on the parameters given, at least for heatmap and heatmap.2. Reading the help pages for heatmap and heatmap.2 will be helpful here. I generally recommend that before someone uses a new function in R or bioconductor, that he read the help page, although I have been guilty of not doing that myself at points. Sean

ADD REPLY • link 18.6 years ago Sean Davis 21k