importing RSEM isoform to Gene Name with tximport
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luca.s ▴ 10
Last seen 4 months ago

Hi all, I am willing to import RSEM sample.isoforms.results files with tximport and have transcript level information summarized to gene level (Gene Name). The endpoint is to perform differential expression analysis with either DESeq2 or edgeR. To this end, I am planning to provide a tx2gene file in which each transcript points to the corresponding Gene Name. Is the code below correct? Please accept my apologies for this basic question, but I am new in the field, and I want to make sure I am doing things correcty. Thanks for the help

Code should be placed in three backticks as shown below

txi <- tximport(files, type="rsem",tx2gene = tx2gene)

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
tximport • 472 views
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Just showing your code without showing what the objects are is not helpful at all. I mean technically that's how you do things, but what are 'files' and what is tx2gene? If they are the right things, then yes you are doing the right thing. If they are not the right things then no, you aren't.

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Right, sorry for the poor comunication, and thank you for your time. Files is a character vector containing the paths of the files, tx2gene is an object generated with the read_csv function on a csv file containing the matchings between transcripts and gene names. I put the first 2 rows of the tx2gene below. A tibble: 250,912 x 2 TXNAME GENEID

<chr> <chr>
1 ENST00000000233.10 ARF5
2 ENST00000000412.8 M6PR

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Last seen 59 minutes ago
United States

IIRC RSEM also outputs the sample.gene.results file as well. So in general you can read in the isoforms file if you want DTE or the gene files if you want DGE. Or you can assume tximport will do a better job of collapsing and do what you have done.


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