Question: How can I import data generated from different sources (salmon and gene count matrix) to generate DESeqDataSet object?
0
gravatar for Di Yang
4 months ago by
Di Yang0
Di Yang0 wrote:

I've got quant.sf files generated by salmon for some samples, and others are gene count matrix files downloaded from web. Is it possible to import them together to generate a DESeqDataSet object? Thx

deseq2 • 100 views
ADD COMMENTlink modified 4 months ago by Michael Love25k • written 4 months ago by Di Yang0
Answer: How can I import data generated from different sources (salmon and gene count ma
1
gravatar for Michael Love
4 months ago by
Michael Love25k
United States
Michael Love25k wrote:

To be safe, I would just take the counts from the tximport list and cbind() them with your other counts matrix. Basically, you are limited in your analysis options because you only have counts for one dataset. There is not the option to use the methods described and recommended in the tximport paper (length offsets, or counts-from-abundance). You can use tximport to import the counts, but just use txi$counts. And then you are just using observed counts in both datasets with no length offset. This is often not a problem (as we note in the paper), but the other tximport methods protect against bias from changes in the effective length of the feature across the samples.

ADD COMMENTlink written 4 months ago by Michael Love25k
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