[BioC] help with DESeq

[Akula, Nirmala (NIH/NIMH) [C]]

Hi,

Below are details of the countsTable and phenotype file.

> head (countsTable)
          bipolar1 bipolar2 bipolar3 bipolar4 control1 control2 control3
NM_000014    13019    23895    33315    13370    26488    25620    31899
NM_000015        5        6        9        1        4        6        5
NM_000016     2932     3316     2874     3320     3195     3017     2312
NM_000017     1156      945     1741     1494      977      800      815
NM_000018    20826    12992    24670    20231    16074    14433    21448
NM_000019     5721     6193     6719     6935     6891     5469     5740
          control4 control5
NM_000014    24253    28868
NM_000015        8        4
NM_000016     3684     2475
NM_000017      738      634
NM_000018    15473    19125
NM_000019     6918     7710

> nisc1Design=read.table("C://Documents and Settings/aaakulan/Desktop/nisc1_phenotype.txt",header=TRUE)
> nisc1Design
         Condition RIN Age Sex
bipolar1   Bipolar 8.8  46   1
bipolar2   Bipolar 6.0  48   1
bipolar3   Bipolar 8.9  73   1
bipolar4   Bipolar 8.0  56   2
control1   Control 8.5  45   1
control2   Control 8.6  57   1
control3   Control 8.0  63   1
control4   Control 8.1  39   2
control5   Control 7.9  56   2

> cdsFull <- newCountDataSet( countsTable,nisc1Design )
> cdsFull <- estimateSizeFactors( cdsFull )
> cdsFull <- estimateDispersions( cdsFull )
Error in rowSums(sapply(tapply((1:ncol(counts))[replicated_sample], factor(conditions[replicated_sample]),  : 
  'x' must be an array of at least two dimensions
> 

Thank you very much.

Regards,
Nirmala

________________________________________
From: Simon Anders [anders at embl.de]
Sent: Monday, December 12, 2011 3:11 PM
To: Akula, Nirmala (NIH/NIMH) [C]; bioconductor at r-project.org
Subject: Re: [BioC] help with DESeq

Dear Nirmala

> We have 4 cases and 5 controls. We would like to add RIN number as one of the covariates to the data analysis. Here is my code which gives errors:
>
>> countsTable=read.table("4Cases_5Controls_counts.txt",header=TRUE)
>> cdsFull<- newCountDataSet( countsTable, nisc1Design )
>> cdsFull<- estimateSizeFactors( cdsFull )
>> cdsFull<- estimateDispersions(cdsFull,"pooled")
>> Error in rowSums(sapply(tapply((1:ncol(counts))[replicated_sample], factor(conditions[replicated_sample]),  :
>>     'x' must be an array of at least two dimensions

At the very least, tell us what is the variables you use to construct
the CountDataSet, i.e., post the content of 'nisc1Design' and the head
of 'countsTable'.

   Simon