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Old 11-07-2011, 09:07 AM   #1
stephenhart
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Location: Europe

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Question error in DESeq analysis

Hello,

I have RNA-seq data, which I am trying to analyze with DESeq. My file (.csv) appears to be correct

>head(myfile)
"
gene_id VZ_w13 VZ_w14a VZ_w14b VZ_w15a VZ_w15b VZ_w16a
1 ENSG00000253101 0 0 0 0 0 0
..."

However, when I try

>cds <- newCountDataSet(myfile,conds)

I get the following error message:

"Error in newCountDataSet(myfile, conds) : The countData is not integer."

The problem, as far as I can tell, is that my data are numerical, not integer, because when I run

>str(myfile)
"'data.frame': 53507 obs. of 14 variables:
$ VZ_w13 : num 0 0 0 0 8 0 0 0 0 0 ..."

Does anyone have a way to make my data integer, not numerical? As you can see, the data are in fact integers.

Thanks,
Stephan
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Old 11-07-2011, 09:54 AM   #2
Dethecor
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Default What about as.integer

If that is really the problem then applying as.integer to your columns should work (note that: as.integer(12.9) == 12)

Cheers,
Paul
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Old 11-07-2011, 10:12 AM   #3
stephenhart
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Default

Excuse my ignorance. How do I apply as.integer to my columns?
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Old 11-07-2011, 11:57 PM   #4
Dethecor
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Default Example

Hi,

here a toy example, which you can just transfer to your data-set:

Code:
> data.frame(SomeValue=seq(0,2,0.4))
  SomeValue
1       0.0
2       0.4
3       0.8
4       1.2
5       1.6
6       2.0
> the.data <- data.frame(SomeValue=seq(0,2,0.4))
> the.data$SomeValue
[1] 0.0 0.4 0.8 1.2 1.6 2.0
> as.integer(the.data$SomeValue)
[1] 0 0 0 1 1 2
> the.data$SomeValue <- as.integer(the.data$SomeValue)
> the.data$SomeValue
[1] 0 0 0 1 1 2
Basically you just apply the function to the column and then replace the column with the result. If you have many columns you might want to use the apply function, which you would do like this:
Code:
> the.data <- data.frame(SomeValue=seq(0,2,0.4), AnotherValue=seq(4,6,0.4))
> the.data
  SomeValue AnotherValue
1       0.0          4.0
2       0.4          4.4
3       0.8          4.8
4       1.2          5.2
5       1.6          5.6
6       2.0          6.0
> apply( the.data, 2, as.integer )
     SomeValue AnotherValue
[1,]         0            4
[2,]         0            4
[3,]         0            4
[4,]         1            5
[5,]         1            5
[6,]         2            6
When in doubt, use the R-help system to find out about things.

Cheers,
Paul
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Old 11-08-2011, 01:05 AM   #5
areyes
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Default

Hi Stephen, looks like the first column of your data are the geneIDs (not integers). Just remove this column and it should be ok. You could use the row.names option when reading the file.
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Old 11-08-2011, 02:55 AM   #6
stephenhart
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Default

Got it working now. Thanks for your help.
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