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Question: Heatmaps for one sample?
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gravatar for Sarah Bonnin
8.2 years ago by
Sarah Bonnin10
Sarah Bonnin10 wrote:
Dear list, I have a short question: I'm performing heatmaps on lists of genes selected as being differentially expressed on a set of 4 technical replicates (from an Agilent gene expression 2 colors experiment). As technical replicates are behaving very similarly, I am taking the median values of the replicates log2ratios, and basically trying to get a heatmaps that would display only one column, being the median value, and the genes on lines. I'm using heatmap.2 which doesn't draw heatmaps for data containing less than 2 columns and 2 rows, so I was wondering if there was a function which does this? I know that it doesn't make so much sense, especially not using biological replicates, but it has a more "visual" goal! Thank you in advance! Sarah
ADD COMMENTlink modified 8.2 years ago by Thomas Girke1.6k • written 8.2 years ago by Sarah Bonnin10
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gravatar for Thomas Girke
8.2 years ago by
Thomas Girke1.6k
United States
Thomas Girke1.6k wrote:
You can trick it by replicating the single column/vector to a matrix of two columns containing the same values. The result in the heatmap will look like a single column. Thomas On Wed, Jul 28, 2010 at 11:04:01AM +0200, Sarah Bonnin wrote: > Dear list, > > I have a short question: I'm performing heatmaps on lists of genes selected as being differentially expressed on a set of 4 technical replicates (from an Agilent gene expression 2 colors experiment). > > As technical replicates are behaving very similarly, I am taking the median values of the replicates log2ratios, and basically trying to get a heatmaps that would display only one column, being the median value, and the genes on lines. > > I'm using heatmap.2 which doesn't draw heatmaps for data containing less than 2 columns and 2 rows, so I was wondering if there was a function which does this? > > I know that it doesn't make so much sense, especially not using biological replicates, but it has a more "visual" goal! > > Thank you in advance! > > Sarah > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 8.2 years ago by Thomas Girke1.6k
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gravatar for Sean Davis
8.2 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Wed, Jul 28, 2010 at 5:04 AM, Sarah Bonnin <sbonnin@crg.es> wrote: > Dear list, > > I have a short question: I'm performing heatmaps on lists of genes selected > as being differentially expressed on a set of 4 technical replicates (from > an Agilent gene expression 2 colors experiment). > > As technical replicates are behaving very similarly, I am taking the median > values of the replicates log2ratios, and basically trying to get a heatmaps > that would display only one column, being the median value, and the genes on > lines. > > I'm using heatmap.2 which doesn't draw heatmaps for data containing less > than 2 columns and 2 rows, so I was wondering if there was a function which > does this? > > I know that it doesn't make so much sense, especially not using biological > replicates, but it has a more "visual" goal! > > I'd consider using a simple bar chart or a waterfall plot. Sean [[alternative HTML version deleted]]
ADD COMMENTlink written 8.2 years ago by Sean Davis21k
Hi, how about something like: > mat = t(matrix(rnorm(100))) > image(mat) needs some tuning of colors and axis labels of course. see ?image Cheers Michael Am Jul 28, 2010 um 6:09 PM schrieb Sean Davis: > On Wed, Jul 28, 2010 at 5:04 AM, Sarah Bonnin <sbonnin at="" crg.es=""> wrote: > >> Dear list, >> >> I have a short question: I'm performing heatmaps on lists of genes selected >> as being differentially expressed on a set of 4 technical replicates (from >> an Agilent gene expression 2 colors experiment). >> >> As technical replicates are behaving very similarly, I am taking the median >> values of the replicates log2ratios, and basically trying to get a heatmaps >> that would display only one column, being the median value, and the genes on >> lines. >> >> I'm using heatmap.2 which doesn't draw heatmaps for data containing less >> than 2 columns and 2 rows, so I was wondering if there was a function which >> does this? >> >> I know that it doesn't make so much sense, especially not using biological >> replicates, but it has a more "visual" goal! >> >> > I'd consider using a simple bar chart or a waterfall plot. > > Sean > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 8.2 years ago by Michael Dondrup550
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