[BioC] problem with EdgeR script

[Ryan]

What is unclear about the error message? R is telling you that you must 
have unique row names for a data frame. This suggests that your data may 
have multiple rows of data for the same gene, which is a data issue.

On 3/25/14, 5:13 PM, Jim Tepperman [guest] wrote:
> I am trying to run an EdgeR script that I have been using for several years.  I am getting an error message early on in the script and cannot figure out what is wrong.  Please advise.
>
>   -- output of sessionInfo():
>
>
> The downloaded binary packages are in
> 	/var/folders/Fx/FxdWG0DyE3eRfY72Zl3JxU+++TI/-Tmp-//RtmpoQbYDm/downloaded_packages
>> library(limma)
>> library (edgeR)
>> mydata<-read.delim(file="wt_vs_pifq.txt",head=TRUE)
>> head (mydata)
>        locus WT1A WT1B WT2A WT2B WT3A WT3B PQ1A PQ1B PQ2A PQ2B PQ3A PQ3B
> 1 AT1G01010   88  117   87  105   76   69   54   24   58   52   68   57
> 2 AT1G01020   36  156   49   49   89   46   53   34   70   54   63   66
> 3 AT1G01030    8   15   12    8    8   11    6    6    7    9   15    5
> 4 AT1G01040   42  120   94   47   85   63   27   15   63   34   49   54
> 5 AT1G01046    0    0    0    0    0    0    0    0    0    0    0    0
> 6 AT1G01050  461  876  424  606  452  369  358  168  348  446  299  285
>> raw.data<- mydata
>> names(raw.data)
>   [1] "locus" "WT1A"  "WT1B"  "WT2A"  "WT2B"  "WT3A"  "WT3B"  "PQ1A"  "PQ1B"  "PQ2A"  "PQ2B"  "PQ3A"  "PQ3B"
>> d<-raw.data[,2:13]
>> rownames(d)<-raw.data[,1]
> Error in `row.names<-.data.frame`(`*tmp*`, value = value) :
>    duplicate 'row.names' are not allowed
> In addition: Warning message:
> non-unique value when setting 'row.names': ‘’
>
> --
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>
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