z0on
commented
2 hours ago Hi Megs - afaik nobody ever saw this error, and there were no recent changes to the repo, so it sounds something is wrong with formatting of your input files. Can you please share them? (or the fist 100 lines maybe) Misha
On Oct 22, 2024, at 3:00 PM, Megs @.***> wrote:
Hi Dr. Matz, I keep running into an error regarding row names when I am running gomwuPlot. I can successfully run the stats function with the following files (plus the files required from GO_MWU) blue_DEfold.csv https://github.com/user-attachments/files/17481339/blue_DEfold.csv Casxa_GO.txt https://github.com/user-attachments/files/17481369/Casxa_GO.txt but a .tab
I get the following output files: MWU_BP_blue_DEfold.csv https://github.com/user-attachments/files/17481400/MWU_BP_blue_DEfold.csv BP_blue_DEfold.csv https://github.com/user-attachments/files/17481401/BP_blue_DEfold.csv but when I try to run the plot function, I get the following error: Error in .rowNamesDF<-(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique values when setting 'row.names': ‘0/16 ’, ‘0/7 ’, ‘0/8 ’, ‘1/5 ’, ‘5/9 ’, ‘6/11 ’, ‘7/5 ’, ‘8/6 ’, ‘8/7 ’, ‘8/8 ’, ‘9/5 ’, ‘9/6 ’
I have traced it back to (at least most likely) to the following lines in the function:
hist(rsq$value) totSum=length(unique(rsq$seq[abs(rsq$value)>=absValue])) row.names(goods)=paste(good.len,"/",pv[pv$term %in% goods.names,]$nseqs," ",pv[pv$term %in% goods.names,]$name,sep="") row.names(heat)=paste(good.len,"/",pv$nseqs," ",pv$name,sep="") row.names(diss.goods)=paste(good.len,"/",pv[pv$term %in% goods.names,]$nseqs," ",pv[pv$term %in% goods.names,]$name,sep="")
but i cannot seem to determine how to fix the problem. If I remove the lines that contain an NA from MWU_BP_blue_DEfold.csv, sometimes I can get past the error, but not always. It has occurred for BP and CC, but it seems like MF works okay. Any suggestions?
Thanks for keeping this repository up to date and all your efforts!
Megan
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mem0294
Hi Dr. Matz, I keep running into an error regarding row names when I am running gomwuPlot. I can successfully run the stats function with the following files (plus the files required from GO_MWU) blue_DEfold.csv Casxa_GO.txt but a .tab
I get the following output files: MWU_BP_blue_DEfold.csv BP_blue_DEfold.csv
but when I try to run the plot function, I get the following error: Error in
.rowNamesDF<-(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique values when setting 'row.names': ‘0/16 ’, ‘0/7 ’, ‘0/8 ’, ‘1/5 ’, ‘5/9 ’, ‘6/11 ’, ‘7/5 ’, ‘8/6 ’, ‘8/7 ’, ‘8/8 ’, ‘9/5 ’, ‘9/6 ’I have traced it back to (at least most likely) to the following lines in the function:
#hist(rsq$value) totSum=length(unique(rsq$seq[abs(rsq$value)>=absValue])) row.names(goods)=paste(good.len,"/",pv[pv$term %in% goods.names,]$nseqs," ",pv[pv$term %in% goods.names,]$name,sep="") row.names(heat)=paste(good.len,"/",pv$nseqs," ",pv$name,sep="") row.names(diss.goods)=paste(good.len,"/",pv[pv$term %in% goods.names,]$nseqs," ",pv[pv$term %in% goods.names,]$name,sep="")but i cannot seem to determine how to fix the problem. If I remove the lines that contain an NA from MWU_BP_blue_DEfold.csv, sometimes I can get past the error, but not always. It has occurred for BP and CC, but it seems like MF works okay. Any suggestions?
Thanks for keeping this repository up to date and all your efforts!
Megan