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': ?????? -- Sent via the guest posting facility at bioconductor.org.

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': ?????? > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor