Merge two data sets
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4.5 years ago
saj98 ▴ 130

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

RNA-Seq R • 1.6k views
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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.

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R also has a merge function that is useful, and you can merge by gene ID.

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Hello I used merge command, but I got this error message, any help or suggestion

> CP1.df <- read.csv(file.choose(), header = TRUE, sep = ",")
> CP2.df <- read.csv(file.choose(), header = TRUE, sep = ",")
> X=merge(CP1.df,CP2.df)
Error: cannot allocate vector of size 4.9 Gb
In addition: Warning messages:
1: In expand.grid(seq_len(nx), seq_len(ny)) :
  Reached total allocation of 20388Mb: see help(memory.size)
2: In expand.grid(seq_len(nx), seq_len(ny)) :
  Reached total allocation of 20388Mb: see help(memory.size)
3: In expand.grid(seq_len(nx), seq_len(ny)) :
  Reached total allocation of 20388Mb: see help(memory.size)
4: In expand.grid(seq_len(nx), seq_len(ny)) :
  Reached total allocation of 20388Mb: see help(memory.size)
>
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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:

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did you try passing in a by argument to merge

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check join in bash

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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.

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Do you see why it initially failed, expanding to > 20Gb, though?

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