Trouble opening .csv files

Q&A
1

Hello,

I have 2 questions:

  1. Do others have problems opening RNAseq transcript .csv files? I have tried everything to open them, and my computer keeps “running out of memory” before the file opens.
  2. Why does the CCLE have genes in columns and cell lines in rows? It seems like it would be easier to work with the genes if it were the other way around
2

Agreed. Excel only allows 16,384 columns of data, and most all of the download files exceed that in gene number. At least in the custom downloads page, would it be possible to default to the matrix where the genes are in rows and cell lines in columns? Or at least provide this as an option? Then there would be no issues for the Excel users.

3

FYI / be aware - if you use excel for this data in general - regardless of column/row orientation - excel will convert some of the gene symbols into dates/times, and then you won’t easily be able to match them up with other datasets and/or will have trouble interpreting the results.

It might make sense to check out R / Rstudio, the interface has gotten quite user friendly. It’s not excel and there will be a learning curve, but you’ll also gain a ton of functionality.

4

Thanks for this response. I have no experience with R. Could I use Rstudio to open the file and then copy paste the parts I need into excel?

Thanks

Jim

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5

Thanks. I agree. The files are not user-friendly at all. I can’t get one to open even with specific software designed to open csv files.

Jim

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6

Hi dllahr,

I took your advice to learn R. Working on downloading the CCLE_RNAseq_reads and getting this data into a R dataframe to work with.
Can you get all of the data from a .txt file to an R dataframe? If this is not good, how do you download the data from ccle in a format that can be imported into R?
Thanks

1 Like
7

Yes! In my experience that is exactly the right way to do it - load the data from the file into data.frame. Here’s a tutorial specific to that you might find useful:
https://swcarpentry.github.io/r-novice-inflammation/11-supp-read-write-csv/index.html

1 Like
8

Thanks very much.

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