use control_condition in heatmap with cummeRbund
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@domenicosomma-12703
Last seen 11 months ago

Hi,

these are my samples:

> samples(cuff_data)
  sample_index sample_name sample_name parameter value
1            1     S80A_0h        <NA>      <NA>  <NA>
2            2     S80A_3h        <NA>      <NA>  <NA>
3            3       wt_0h        <NA>      <NA>  <NA>
4            4       wt_3h        <NA>      <NA>  <NA>

The cummeRbund manual says:

csHeatmap : Creates a ggplot plot object with a geom_tile layer of FPKM values per feature and sample

argument: control_condition: A character argument indicating which condition should be used as the denominator for fold change. (e.g. "Day0", "Control", etc)

But I can't use it

h<-csHeatmap(myGenes, clustering='row',control_condition="S80A_0h")
h<-csHeatmap(myGenes, clustering='row',control_condition="wt_0h")
h<-csHeatmap(myGenes, clustering='row',control_condition=1)
h<-csHeatmap(myGenes, clustering='row',control_condition=3)

Give me always the same heatmap. Could you show me where is the mistake?

cummerbund heatmap • 1.3k views
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