DESeq2 error message on R3.3

Question

[ta_awwad]

Hi, I ran the following script on R version 3.2 and everything was fine:

conds<- c("kd1","kd1","kd2","kd2","GFP","GFP")

Design<-data.frame(condition=conds,
                   row.names=paste(conds,rep(c(1,2),3),
                   sep="_"))
dds <- DESeqDataSetFromMatrix(countData = assay(se),
                             colData = Design,
                             design = ~ condition)

however, when I updated R into 3.3 I start getting the following error message:

Error in FUN(X[[i]], ...) : 
  assay colnames() must be NULL or equal colData rownames()

I tried to follow many solutions but non of them worked .

can anyone help

thanks much

Answer 1

[Devon Ryan]

So what's colnames(se)?

[ta_awwad]

   >  colnames(se)
[1] "kd1_1.bam" "kd1_2.bam" "kd2_1.bam"  "kd2_2.bam"  "GFP_1.bam"  
[6] "GFP_2.bam"

whereas,

> Design
                  condition
kd1_1          kd1
kd1_2          kd1
kd2_1          kd2
kd2_2          kd2
GFP_1        GFP
GFP_2        GFP

[Devon Ryan]

There's your problem then.

[ta_awwad]

thanks I solved the problem

[ta_awwad]

got it .. thanks much