Entering edit mode
7.4 years ago
saj98
▴
140
Hello everyone
I have two RNA seq experiments, one done on tissue and the second one done on cells. I am looking to do cross correlation between the two experiments. I have CSV file for each experiment. I am interested to merge the two files in one CSV file. How I can merge the two files with matching the gene IDs? I am looking to do this step because I am interested to calculated the correlation of gene expression between invitro and invivo.
Thanks for help
You can read CSV files into R separately, and use the gene IDs as rownames of data frame, then you can use
cbind
to merge two data frame.R also has a merge function that is useful, and you can merge by gene ID.
Hello I used merge command, but I got this error message, any help or suggestion
I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:
did you try passing in a
by
argument tomerge
check join in bash
Hello I got the figured out how to solve it, and I am sharing it with you
exporttab <- merge(x=dwd_nogap, y=dwd_gap, by.x='x1', by.y='x2', fill=-9999), and it was very useful.
Do you see why it initially failed, expanding to > 20Gb, though?