[BioC] NOISeq initialization problem

[Sonia Tarazona]

Dear Sara,

We think there is no problem at all with your data. You can keep on 
doing your analysis following the manual and we don't expect you to have 
any kind of problem. You got an error message because you are applying 
the head() function to the object generated by readData(). You do not 
have to do that with this kind of objects. Just type the name of the 
object and a little summary will be shown.

We appreciate your interest and we will fix NOISeq as soon as possible 
so it does not return this error message anymore.

Best regards,

Sonia Tarazona





On 10/11/2012 07:19 PM, Dan Tenenbaum wrote:
> 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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-- 
Sonia Tarazona
PhD Student
Bioinformatics & Genomics Department
Centro de Investigación Príncipe Felipe
http://bioinfo.cipf.es