I have a gene expression dataset in Excel/CSV file with 200 columns and 22,000 rows. What will be the best way to switch columns and rows. (This cannot be done in Excel as it supports maximum ~ 16,000 columns)
I want my output as CSV file so that I can load it in Weka.
I don't know programming...So it would be good to know if there is any available tool for this
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written
by
ayanabha.research01 •
Never use excel for bioinformatics stuff!
Use R.
In R:
a <- read.table(file.csv,sep="\t")
b <- t(a)
Hi NicoBxl... I tried this with a small dataset , it seem to work fine...but I guess there are some issues working with such large dataset ..it gives some error
200 x 22,000 should work perfectly ;) What is the amount of RAM you have?
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written
by
Nicolas Rosewick
My laptop has 4GB RAM
should work
Tried..
Giving output like this...confused
[,22239] [,22240] [,22241]
[,22242] [,22243] [,22244] [,22245]
[,22246] [,22247] [,22248] [,22249]
[,22250] [,22251] [,22252] [,22253]
[,22254] [,22255] [,22256]
[,22257] [,22258] [,22259]
[,22260] [,22261] [,22262]
[,22263] [,22264] [,22265]
[,22266] [,22267] [,22268]
[,22269] [,22270] [,22271]
[,22272] [,22273] [,22274]
[,22275] [,22276] [,22277]
[,22278] [,22279] [,22280] [,22281]
[,22282] [,22283] [,22284]
[ reached getOption("max.print") -- omitted 11 rows ]
Note one little quirk of read.table, it expects the header row to have one less entry than the rest of the file, so if you have a header for the first column, it's going to behave strangely. Also note that you might need to manually add a space to the header after you use write.table, or the header names might not match columns correctly.
Also how do I export the transposed data from R to my desktop as a CSV file?
write.table(b,"out.txt",sep="\t",quote=F)
Tried this code, but its exporting the original file but not the transposed one
Better rewrite a new thread for your question in order to be more specific.
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