This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Error While Combining Multiple Csv
> files <- list.files(pattern=".csv")
> files
[1] "GDS2475.csv"       "GDS2477.csv"       "GSE12594_soft.csv"
[4] "GSE15435.csv"      "GSE20130.csv"     

> data()
> DF <- NULL
> for (f in files) {
+    dat <- read.csv(f, header=T, sep="\t", na.strings="", 
+ colClasses="character")
+    DF <- rbind(DF, dat)
+ }
Error in match.names(clabs, names(xi)) : 
  names do not match previous names
>

I saw this script for reading multiple csv files and combining. I got the error in the bottom. Any suggestions would be helpful, because I am new to R.

r microarray
• 4,006 views • link
updated by Ram Ram • written by Bmusungu • Bmusungu

Are the columns the same length for each file?

• 0 views • link
written by Zev.Kronenberg Zev.Kronenberg

I would say: "are the number of columns the same..." ;-)

• 0 views • link
written by Manu Prestat Manu Prestat

No, because I've been trying to combine microarray soft files together.

• 0 views • link
written by Bmusungu • Bmusungu

This is a basic R question with little bioinformatics research content. Closing as off-topic: try stackoverflow.com.

• 0 views • link
written by Neilfws Neilfws

1 answer

Hi, I'm not sure it's the best place for "R only" questions here, but let's give it a try: first, perhaps the data() line is unuseful. I think the error here is due to rbind() (means combine by rows) which checks your dataframes have the same column names. Try by putting the same names, for instance by adding in the loop a colnames() call:

for (f in files) {
 dat <- read.csv(f, header=T, sep="\t", na.strings="", colClasses="character")
 colnames(dat)<-c("col1","col2","col3")
 DF <- rbind(DF, dat)
 }

If it's not a good answer, try on R-help, or stackoverflow.

• 1 views • link
written by Manu Prestat Manu Prestat

Log in to answer this question.

More posts like this