Hello,
I am writing to ask your help in regard to performing differential analysis to analyze miR RNA-seq data. I have miRNA seq data and I have analyzed in the following way-
Would you be so kind to help me with this issue?
Thanks in advance
MD
You should specify the exact error while executing Deseq2. There can be multiple source of the errors.
Mayur Doke, DESeq2, or edgeR use like input raw counts of transcripts (mRNA, miRNA, and other features). So then, you want to guarantee this condition. But how Asgar Hussain wrote, you need to tell us what's error did you found.
Best regards.
The raw count of miRNA must be an integer. If you did this, the error may come from DEseq2. Please tell us the exact error while executing Deseq2.
Thank you for your reply Wentao Cai, André Nicolau Aquime Gonçalves and Asgar Hussain . I am sorry for the delayed response. Please find below error that DESeq2 gave me-
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
duplicate 'row.names' are not allowed
Calls: get_deseq_dataset ... lapply -> lapply -> FUN -> read.delim -> read.table
Mayur Doke You have some miRNAs with more than one rows. Remove the redundant miRNAs or you can set "check.names =False" while reading expression file.
This error isn't from DESeq2 package. You need to check your expression file to remove duplicated gene symbols. Load your file with rownames = FALSE parameter. So, then you can try to run this:
#Colapse symbols that are duplicated by taking the one with higest expression
exp$meanG
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Nucleic Acids
- RNA
- Small RNA
- microRNA