Why numebers in counts.matrix is not integer?

[Xiaopei Su]

Hi Brian and all,

I am doing a time course study using DESeq package. In the process of importing raw counts to R, I got an error said: 

Error in DESeqDataSet(se, design = design, ignoreRank) : 

  some values in assay are not integers

The I noticed the numbers in counts.matrix is not integer. But I thought this file is the raw counts number? Why it's not integer? 

Is there anyway I can use this file? 

Thank you in advance! 

Best regards,

Xiaopei 

[Brian Haas]

The counts are fractionally assigned by the various abundance estimation methods, as a way of dealing with multi-mapped reads.

You can convert them to integer values in R.  If you don't find out how via google, I can provide some hints.

best,

~b

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[Xiaopei Su]

Thank you Brian! 

Can I use as.integer(matrix) to do this? 

Best regards,

Xiaopei 

On Thursday, March 10, 2016 at 4:52:01 PM UTC, Brian Haas wrote:

The counts are fractionally assigned by the various abundance estimation methods, as a way of dealing with multi-mapped reads.

You can convert them to integer values in R.  If you don't find out how via google, I can provide some hints.

best,

~b

On Thu, Mar 10, 2016 at 11:40 AM, Xiaopei Su <suxi...@gmail.com> wrote:

Hi Brian and all,

I am doing a time course study using DESeq package. In the process of importing raw counts to R, I got an error said: 

Error in DESeqDataSet(se, design = design, ignoreRank) : 

  some values in assay are not integers

The I noticed the numbers in counts.matrix is not integer. But I thought this file is the raw counts number? Why it's not integer? 

Is there anyway I can use this file? 

Thank you in advance! 

Best regards,

Xiaopei 

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[Brian Haas]

fyi, in case it helps (note I'm not an R guru, but an R survivor):

> m = matrix(c(1.1, 2.2, 3.3, 4.4, 5.5, 6.6), byrow=T, ncol=2)
> m
     [,1] [,2]
[1,]  1.1  2.2
[2,]  3.3  4.4
[3,]  5.5  6.6
> as.integer(m)
[1] 1 3 5 2 4 6

> apply(m, 1:2, round)

     [,1] [,2]

[1,]    1    2

[2,]    3    4

[3,]    6    7

> 

[Xiaopei Su]

That's good enough for me, thank you very much! 

Best regards,

Xiaopei