[gareth.lim]

My experiment is complicated (at least in my mind =) ). I have three time points (0,24,48 hrs) and two conditions (siControl and siTarget) for a total of 6 groups. I'm trying to see how knockdown of my target affects the transcriptome at each time point.

This information is the closest I can find online that describes how to make a log2-fold change heat map and a dendrogram.... but I'm having some troubles. Can anyone please help?

A few questions so far:

1. sigGenes <- getSig(cuff,'BY4741','ino80',alpha=0.05,level='genes')
-Why were only two of your groups selected here and not the whole data set? Does this impact the final result?

2. db <- logFC(db,mutants=mut,WT=WT,logBase=2,pseudo=1)
-when i enter this, I get an error message: Error in db[, mutants] : incorrect number of dimensions

[gareth.lim]

Sorry clicked too fast...

Sorry I should add that so far I have done this:
>WT<-"C1"
> mut<-c("C2","C3","C4","C5","C6")

My experiment is complicated (at least in my mind =) ). I have three time points (0,24,48 hrs) and two conditions (siControl and siTarget) for a total of 6 groups. I'm trying to see how knockdown of my target affects the transcriptome at each time point.

This information is the closest I can find online that describes how to make a log2-fold change heat map and a dendrogram.... but I'm having some troubles. Can anyone please help?

A few questions so far:

1. sigGenes <- getSig(cuff,'BY4741','ino80',alpha=0.05,level='genes')
-Why were only two of your groups selected here and not the whole data set? Does this impact the final result?

2. db <- logFC(db,mutants=mut,WT=WT,logBase=2,pseudo=1)
-when i enter this, I get an error message: Error in db[, mutants] : incorrect number of dimensions