Hi,

I am using FourCseq with one 4C experiment with 2 biological replicates and 2 view points.:

DataFrame with 4 rows and 5 columns
    viewpoint condition replicate              bamFile sequencingPrimer
  <character>  <factor> <numeric>          <character>      <character>
1        FLC1         A         1 INDEX_1_3.sorted.bam            first
2        FLC1         A         2 INDEX_1_4.sorted.bam            first
3        FLC2         B         1 INDEX_1_5.sorted.bam            first
4        FLC2         B         2 INDEX_1_6.sorted.bam            first

When I run:

fcf <- getZScores(fc)

I get the following error:

Error in getZScores(fc) :
  None or more than one viewpoint are contained in the 'FourC' object.
         Use a 'FourC' object that contains only one viewpoint.

The pipeline doesnt support multiple view points?

Could you please help me with this if it is possible to run it with 2 viewpoints ?

Best Regards

Dimitris

I think that i found the solution which is :

fcf1 <- getZScores(fc[,c("FLC1_A_1", "FLC1_A_2")])
fcf2 <- getZScores(fc[,c("FLC2_B_1", "FLC2_B_2")])

i had to select each viewpoint with his replicates in order to have the Zscorres. Thanks for the inspiration !