Question

Merge problems in R

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FWNL15 • 0

@aba2f833

Last seen 3.2 years ago

Netherlands

I'm having trouble with merging two datasets in R. The first part is not giving any problems, but in the second part I get an error that a uniquely valid column must be specified. It is actually an existing column, so I don't understand why it is not valid. Does anyone have a clue?

# Data merge and save for further processing
> df1<- as.data.frame(mynormGSE117852)
> df2<- as.data.frame(mynormSPN)
> merged_panNET_SPN<- merge(df1, df2, by.x="row.names", by.y="row.names")
> rownames(merged_panNET_SPN) <- merged_panNET_SPN[,1]
> merged_panNET_SPN[,1] <- NULL

> tmerged_panNET_SPN<-as.data.frame(t(merged_panNET_SPN))
> annoGEO<- merge(PD_panNET_SPN[,c(1,3)], tmerged_panNET_SPN, by.x="Sample_Name", by.y="row.names", sort = FALSE)
Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column

methylationArrayAnalysis ChAMP MethylationArrayData • 3.9k views

ADD COMMENT • link 3.4 years ago FWNL15 • 0

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What is colnames(PD_panNET_SPN) and rownames(tmerged_panNET_SPN) ?

ADD REPLY • link 3.4 years ago Basti ▴ 780

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tmerged_panNET_SPN = dataframe of two datasets which are merged above.

PD_panNET_SPN= a PD file of the two merged datasets

ADD REPLY • link 3.4 years ago FWNL15 • 0

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I was asking for the output of colnames(PD_panNET_SPN) and rownames(tmerged_panNET_SPN), we need to check your column and rownames, without this it is impossible to help you

ADD REPLY • link 3.4 years ago Basti ▴ 780

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Sorry, good one!

> colnames(PD_panNET_SPN)
 [1] "ï..X.Header." "X"            "X.1"          "X.2"          "X.3"          "X.4"          "X.5"         
 [8] "X.6"          "X.7"          "X.8"          "X.9"          "X.10.."      
> rownames(tmerged_panNET_SPN)
 [1] "A_mk11"   "A_mk12"   "A_mk4"    "A_mk47"   "AM1_mk36" "AM1_mk53" "D_LS21"   "D_mk18"   "D_mk26"   "D_mk34"  
[11] "D_mk42"   "D_mk51"   "D_mk9"    "DM1_LS7"  "DM1_mk17" "DM1_mk44" "DM1_mk45" "DM1_mk52" "M1_LS1"   "WT_LS27" 
[21] "WT_LS35"  "WT_LS39"  "WT_LS65"  "WT_mk13"  "WT_mk15"  "WT_mk19"  "WT_mk21"  "WT_mk27"  "WT_mk39"  "WT_mk49" 
[31] "WT_mk50"  "WT_mk8"   "SPN2T"    "SPN3T"    "SPN4T"    "SPN5T"    "SPN6T"    "SPN7T"    "SPN8T"    "SPN9T"   
[41] "SPN10T"   "SPN11T"   "SPN12T"   "SPN13T"   "SPN14T"   "GCT4"     "GCT5"

Guess I have to change colnames in PD file if I look at this right now?

ADD REPLY • link 3.4 years ago FWNL15 • 0

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You don't have any Sample_Name column inside your PD_panNET_SPN dataframe so it can't work

ADD REPLY • link 3.4 years ago Basti ▴ 780

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Yes there is one but not in the right place I see right now. Thanks, I know how to solve this now!

ADD REPLY • link 3.4 years ago FWNL15 • 0