tximport with salmon bootstraps and edger/deseq2
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Themis • 0
@Themis-24410
Last seen 10 months ago

Enter the body of text here

Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output
# please also include the results of running the following in an R session
rep <- tximport(files, type =
"salmon",countsFromAbundance="scaledTPM",varReduce=F, txOut =
F,tx2gene=tx2gene,ignoreTxVersion = TRUE)
> names(rep)
[1] "abundance"           "counts"              "infReps"             "length"
[5] "countsFromAbundance"
# From this point on, I have a difficulty on how to use these data on
#edgeR or deseq2, since I don't know how to take the bootstrap data
#into account. I have performed similar analyses using the TPM values
#without bootstraps but I can't really figure how to import them as
#well. Hence, I kindly request if you can propose a way to continue
#with my downstream analysis
sessionInfo( )

tximport • 201 views
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@mikelove
Last seen 8 hours ago
United States

We found in our paper on inferential uncertainty that making use of bootstrap/Gibbs replicates didn't have a huge impact on gene-level analysis (see Fig 2 for example).

If you are interested in transcript-level analysis, I'd recommend to consider the Swish method and vignette, which we've developed from our group particularly for use with tximport / tximeta and making use of the inferential samples: