DESeq - Error: subscript out of bounds

[crh]

Hi,

I'm getting the following error when I try to take a subset from the data for analysis:

> conds
[1] "Ag" "Ti" "Qd" "Zn" "Ctrl"
> head( counts(cds) )
ag ti qd zn ctrl
1 29 14 8 15 16
2 3 2 1 3 2
3 2 1 1 5 0
4 3 2 1 5 1
5 1 1 2 1 1
6 2 1 1 2 4
>cds <- estimateSizeFactors( cds )
> cds2 <- cds[,c("Ag","Ctrl")]
Error: subscript out of bounds


Any suggestions?

Charles

[NicoBxl]

it's

cds2 <- count(cds)[,c("Ag","Ctrl")]

[vyellapa]

Did you find a solution for this? I am getting the same error and am not sure how to fix it:

> conds
[1] treated untreated
Levels: treated untreated
> cds2 <-cds[,c("treated", "untreated") ]
Error: subscript out of bounds
> cds2 <-count(cds)[,c("treated", "untreated") ]
Error: could not find function "count"
> cds2 <-counts(cds)[,c("treated", "untreated") ]
Error: subscript out of bounds

[Simon Anders]

If you take a asubset from a matrix-like object such as an ExpressionSet or a CountDataSet, using the idiom

cds[,c("a","b","c")]

, the strings "a", "b", "c" are supposed to be column names (here: sample names), not conditions.

[vyellapa]

Thank you, that worked!

[AsoBioInfo]

If you take a asubset from a matrix-like object such as an ExpressionSet or a CountDataSet, using the idiom

cds[,c("a","b","c")]

, the strings "a", "b", "c" are supposed to be column names (here: sample names), not conditions.

Thank you so much! It worked like a charm.... Keep up the good work!

[sheibani]

--------------------------------------------