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Old 11-16-2010, 05:24 AM   #1
crh
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Default DESeq - Error: subscript out of bounds

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
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Old 11-16-2010, 05:41 AM   #2
NicoBxl
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it's

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

Last edited by NicoBxl; 11-16-2010 at 05:44 AM.
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Old 03-15-2012, 04:07 PM   #3
vyellapa
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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
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Old 03-16-2012, 01:23 AM   #4
Simon Anders
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If you take a asubset from a matrix-like object such as an ExpressionSet or a CountDataSet, using the idiom
Code:
cds[,c("a","b","c")]
, the strings "a", "b", "c" are supposed to be column names (here: sample names), not conditions.
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Old 03-16-2012, 12:38 PM   #5
vyellapa
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Thank you, that worked!
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Old 04-18-2012, 04:31 AM   #6
AsoBioInfo
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Quote:
Originally Posted by Simon Anders View Post
If you take a asubset from a matrix-like object such as an ExpressionSet or a CountDataSet, using the idiom
Code:
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!
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Old 07-28-2015, 03:56 AM   #7
sheibani
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--------------------------------------------

Last edited by sheibani; 07-29-2015 at 02:39 AM.
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