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What to do after importing quantification with tximport

I am doing the classic pipeline for DGE Analysis. I have quantified some rna-sequences with Salmon and now I have imported them with tximport package (as the vignette says). I am new to the field and I am stuck at this point. On the vignette, before performing DGE with Deseq2 , they create a sampleTable which must have the same row names as the column names of txi$counts. I don't know why I have to create this table and how Iit can be useful for the analysis. The matrix with gene/counts (txi table) isn't enough ?

Thank you.

r transcriptome de deseq2
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written by dylannicoembros • dylannicoembros

1 answer

You need metadata for your samples. What condition does each sample belong to? That's why you need the colData object.

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written by Trivas • Trivas

I have healty and not-healty sample. I am very confused sorry.

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written by dylannicoembros • dylannicoembros

Basically the variables that you will be using in your model formula should come from the colData, which is constructed from the sampleTable you will create. So, in your case your sampleTable will have one column with a name like health_status and two levels within it, either a healthy or non-healthy and the row names of this table should correspond to the column names of your count table as you also mentioned.

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written by Haci Haci

So basically I have to costruct the sampleTable using the health_status column that I have from my data. And that's it. Thank you for the clarification.

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written by dylannicoembros • dylannicoembros

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