<p>I used the Tximeta vignette to construct a summarised experiment from quant files (salmon, index prepared with NCBI transcriptome).</p>

<p>1)Tximeta return me a non-ranged se (which I am not sure about the real implications)</p>

<p>because of this...
2) I used <code>makeLinkedTxome</code> to link the transcriptome and the gff (local files used in the index creation). </p>

<p>3)run <code>tximeta</code> on the colData to create the summarised experiment <code>se</code></p>

<p>4) <code>seqinfo(se)</code> returns me a NA populated table</p>

<p>5) I summarise to genes (<code>gse</code>)</p>

<p>6) I extracted the gene counts <code>counts &lt;- assay(gse)</code></p>

<p>My questions here are;</p>

<p>a) Are these counts normalised? 
b) If not, how can I normalise them? TMM for example? (CalcNormFactors will not work here right?)</p>

<p>Is there any better way to obtain a normalised count matrix from tximeta? (maybe I don't need to link the transcriptome...)</p>

<p>Any help would be appreciated!
Thank you! and regards,</p>

CC BY-SA 4.0
2020-05-28T10:52:36.993Z
Thank you! so I can use these `counts'  with the pipeline. Perfect! thanks!!!
FrAoJm
<rna-seq>
extracted counts matrix from Tximeta generalized experiment with no linked transcriptome are normalized?
# extracted counts matrix from Tximeta generalized experiment with no linked transcriptome are normalized?

(Asked by: username_0 on 2020-05-27)

I used the Tximeta vignette to construct a summarised experiment from quant files (salmon, index prepared with NCBI transcriptome).

1)Tximeta return me a non-ranged se (which I am not sure about the real implications)

because of this...
2) I used `makeLinkedTxome` to link the transcriptome and the gff (local files used in the index creation).

3)run `tximeta` on the colData to create the summarised experiment `se`

4) `seqinfo(se)` returns me a NA populated table

5) I summarise to genes (`gse`)

6) I extracted the gene counts `counts <- assay(gse)`

My questions here are;

a) Are these counts normalised?
b) If not, how can I normalise them? TMM for example? (CalcNormFactors will not work here right?)

Is there any better way to obtain a normalised count matrix from tximeta? (maybe I don't need to link the transcriptome...)

Any help would be appreciated!
Thank you! and regards,

**Tags:** rna-seq
> **Comments:**
> **username_0**: Thank you! so I can use these `counts'  with the pipeline. Perfect! thanks!!!  

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## 0 answers

