[BioC] NOISeq initialization problem

[Dan Tenenbaum]

I'm CC'ing the maintainer of the NOISeq package who may be able to
answer your question.
Dan


On Thu, Oct 11, 2012 at 1:32 AM, sara wilson [guest]
<guest at bioconductor.org> wrote:
>
> Hi and good day,
>
> I am totally new to R so sorry is my question is so naive.
> I am just following the NOISeq tutorial with my own data set.Below is what I have in order to make the readData:
>
> my data:
>> head(counts)
>              V2 V3  V4  V5 V6  V7 V8  V9
> 1/2-SBSRNA4   3  5   4   4  2   3  1   1
> A1BG        200 93 246 102 86  46 58  85
> A1BG-AS1     24 28  16  32 17  10 19  14
> A1CF          1  1   1   2  1   0  0   1
> A2LD1       100 71  98  97 59 128 88 114
> A2M           5  5  23   1  5   6 10   5
>
>> class(counts)
> [1] "data.frame"
>
> my factors :
>> factors
>      sex
> 1 Female
> 2 Female
> 3 Female
> 4 Female
> 5   Male
> 6   Male
> 7   Male
> 8   Male
>
> and my length :
>> head(mylength)
> 1/2-SBSRNA4        A1BG    A1BG-AS1        A1CF       A2LD1         A2M
>          23                  916         160                    7         755               60
>> class(mylength)
> [1] "integer"
>
> when I run the command readData, without the length property it produces the object but with the length property, there is an error. so there should be problem with that but I do not know what is it.
> Many thanks in advance.
>
>  -- output of sessionInfo():
>
>> noy1 <- readData(data=counts, factors=factors, length= mylength)
>> head(noy1)
> Error in value[[3L]](cond) : invalid 'row.names' length
>   AnnotatedDataFrame 'initialize' could not update varMetadata:
>   perhaps pData and varMetadata are inconsistent?
>
> and then without length:
>
>> noy1 <- readData(data=counts, factors=factors)
>> head(noy1)
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 1 features, 8 samples
>   element names: exprs
> protocolData: none
> phenoData
>   sampleNames: V2 V3 ... V9 (8 total)
>   varLabels: sex
>   varMetadata: labelDescription
> featureData: none
> experimentData: use 'experimentData(object)
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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