<p>By setting <code>type="salmon"</code> you're overriding your settings for things like <code>txIdCol</code>. The various <code>type</code> options (except <code>none</code>) are presets to set things correctly for the output from various programs like <code>salmon</code> or <code>kallisto</code>. If you need to specify custom column names, set <code>type="none"</code>.</p>

<p>As an aside, if I'm interpreting your question correctly you have only two samples in total. You can not perform a meaningful analysis with an unreplicated experiment, so if that is indeed your case then don't waste your time further with this dataset.</p>

CC BY-SA 4.0
2018-05-03T18:06:59.563Z
Thank you, that explains it. As for the lack of replicates this is for an undergraduate research project, and we're just trying to get our R code to work until we get actual data.
wolff
CC BY-SA 4.0
2018-05-03T18:19:47.027Z
Ah download a public dataset and try to reproduce a published analysis with that. If you can set similarish (or better!) results as those published then you're good to go :)
Devon Ryan
CC BY-SA 4.0
2018-05-03T06:57:58.867Z
2018-05-03T06:57:58.867Z
Devon Ryan
<p>I'm trying to run a differential expression analysis of 2 samples of the same species, but with different treatments using DESeq2. I'm using Ensembldb to create a tx2gene dataframe for tximport, however tximport does not select the columns I specify, and instead always selects the tx_biotype leading to the following output:</p>

<pre><code>.                    25_quant    28_quant
nontranslating_CDS    10422.41    10022.74
protein_coding     22196722.59 24002269.26
</code></pre>

<p>I'm running tximport using the following params:</p>

<pre><code>txi_tx &lt;- tximport(files, type = "salmon", tx2gene = tx2gene,
                   txIdCol = "tx_id", geneIdCol = "gene_id")
</code></pre>

<p>I've gotten around this by deleting all columns from my tx2gene DF apart from tx_id and gene_id. However, I think this might be causing problems in the DESeq2 analysis somehow, and I would like to rule out that possibility.</p>

<p>This is what my <code>names(tx2gene)</code> looks like:</p>

<pre><code>"tx_id"            "tx_biotype"       "tx_seq_start"     "tx_seq_end"
"tx_cds_seq_start" "tx_cds_seq_end"  
"gene_id"          "tx_name"
</code></pre>

<p>What am I doing wrong?</p>

<r><ensembl><tximport><tx2gene>
tximport txidcol and geneidcol selecting wrong column
# tximport txidcol and geneidcol selecting wrong column

(Asked by: username_0 on 2018-05-02)

I'm trying to run a differential expression analysis of 2 samples of the same species, but with different treatments using DESeq2. I'm using Ensembldb to create a tx2gene dataframe for tximport, however tximport does not select the columns I specify, and instead always selects the tx_biotype leading to the following output:
.                    25_quant    28_quant
nontranslating_CDS    10422.41    10022.74
protein_coding     22196722.59 24002269.26

I'm running tximport using the following params:
txi_tx <- tximport(files, type = "salmon", tx2gene = tx2gene,
                   txIdCol = "tx_id", geneIdCol = "gene_id")

I've gotten around this by deleting all columns from my tx2gene DF apart from tx_id and gene_id. However, I think this might be causing problems in the DESeq2 analysis somehow, and I would like to rule out that possibility.
This is what my names(tx2gene) looks like:
"tx_id"            "tx_biotype"       "tx_seq_start"     "tx_seq_end"
"tx_cds_seq_start" "tx_cds_seq_end"  
"gene_id"          "tx_name"

What am I doing wrong?

**Tags:** r, ensembl, tximport, tx2gene

---

## 1 answers

### Answer by username_1 on 2018-05-03. Score: 2 | Accepted answer

By setting `type="salmon"` you're overriding your settings for things like `txIdCol`. The various `type` options (except `none`) are presets to set things correctly for the output from various programs like `salmon` or `kallisto`. If you need to specify custom column names, set `type="none"`.

As an aside, if I'm interpreting your question correctly you have only two samples in total. You can not perform a meaningful analysis with an unreplicated experiment, so if that is indeed your case then don't waste your time further with this dataset.

> **Comments:**
> **username_0**: Thank you, that explains it. As for the lack of replicates this is for an undergraduate research project, and we're just trying to get our R code to work until we get actual data.  
> **username_1**: Ah download a public dataset and try to reproduce a published analysis with that. If you can set similarish (or better!) results as those published then you're good to go :)  

---

