<p>Don't know which file was used by cummeRbund for sample names but replacing q1,q2,q3 and q4  with Batis, Blue_silver, Chakwal_50 and Syn_22 for all the files in the directory containing cuffdiff output worked for me. </p>

<p>I used sed language for this as shown below:</p>

<pre><code>sed -i 's/q4/Syn_22/g' *
</code></pre>

<p>Or more generally you can use </p>

<pre><code>sed -i 's/sample_name_shown/sample_name_to_change/g' *
</code></pre>

<p>After that I deleted the sqlite object created by cummeRbund and again created this object using <strong>readCufflinks()</strong> in R.
This time sample names are changed as desired:</p>

<pre><code>samples(cuff)
sample_index sample_name sample_name parameter value
1            1       Batis        &lt;NA&gt;      &lt;NA&gt;  &lt;NA&gt;
2            2 Blue_silver        &lt;NA&gt;      &lt;NA&gt;  &lt;NA&gt;
3            3  Chakwal_50        &lt;NA&gt;      &lt;NA&gt;  &lt;NA&gt;
4            4      Syn_22        &lt;NA&gt;      &lt;NA&gt;  &lt;NA&gt;
</code></pre>

CC BY-SA 4.0
2018-07-28T11:24:25.427Z
2018-07-28T11:24:25.427Z
Ammar Sabir Cheema
<p>I want to analyze RNA seq data using R package <a href="https://bioconductor.org/packages/release/bioc/html/cummeRbund.html" rel="nofollow noreferrer">cummeRbund</a>. Using this package I have a problem changing sample names. When I run this command in cummeRbund</p>

<pre><code>samples(cuff) 
sample_index sample_name sample_name parameter value
1            1          q1        &lt;NA&gt;      &lt;NA&gt;  &lt;NA&gt;
2            2          q2        &lt;NA&gt;      &lt;NA&gt;  &lt;NA&gt;
3            3          q3        &lt;NA&gt;      &lt;NA&gt;  &lt;NA&gt;
4            4          q4        &lt;NA&gt;      &lt;NA&gt;  &lt;NA&gt;
5            5          q5        &lt;NA&gt;      &lt;NA&gt;  &lt;NA&gt;
</code></pre>

<p>It shows q1,q2,q3,q4 and q5 as sample names for the five samples but I want to change the sample names and put following names for the samples Batis, Blue_silver, Chakwal_50, Local_white and Syn_22 for q1,q2,q3,q4 ad q5 respectively. To accomplish this I ran following command:</p>

<pre><code>&gt; samples(cuff) &lt;- c("Batis", "Blue_silver","Chakwal_50","Local_white","Syn_22")
Error in samples(cuff) &lt;- c("Batis", "Blue_silver", "Chakwal_50", "Local_white",  : 
could not find function "samples&lt;-"
</code></pre>

<p>but this command gave error as shown above.</p>

<p>Also the BAM files have same names for all the samples as mentioned above. </p>

<p>How could I change the sample names to desired names in R using cummeRbund? </p>

<p>Or I need to re-run cuffdiff and change the names somewhere else?  </p>

<rna-seq><differential-expression><cummerbund>
Change sample names while using cummeRbund
# Change sample names while using cummeRbund

(Asked by: username_0 on 2018-07-23)

I want to analyze RNA seq data using R package cummeRbund. Using this package I have a problem changing sample names. When I run this command in cummeRbund
samples(cuff) 
sample_index sample_name sample_name parameter value
1            1          q1                
2            2          q2                
3            3          q3                
4            4          q4                
5            5          q5                

It shows q1,q2,q3,q4 and q5 as sample names for the five samples but I want to change the sample names and put following names for the samples Batis, Blue_silver, Chakwal_50, Local_white and Syn_22 for q1,q2,q3,q4 ad q5 respectively. To accomplish this I ran following command:
> samples(cuff) <- c("Batis", "Blue_silver","Chakwal_50","Local_white","Syn_22")
Error in samples(cuff) <- c("Batis", "Blue_silver", "Chakwal_50", "Local_white",  : 
could not find function "samples<-"

but this command gave error as shown above.
Also the BAM files have same names for all the samples as mentioned above. 
How could I change the sample names to desired names in R using cummeRbund? 
Or I need to re-run cuffdiff and change the names somewhere else?

**Tags:** rna-seq, differential-expression, cummerbund

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## 1 answers

### Answer by username_0 on 2018-07-28. Score: 1 | Accepted answer

Don't know which file was used by cummeRbund for sample names but replacing q1,q2,q3 and q4  with Batis, Blue_silver, Chakwal_50 and Syn_22 for all the files in the directory containing cuffdiff output worked for me. 
I used sed language for this as shown below:
sed -i 's/q4/Syn_22/g' *

Or more generally you can use 
sed -i 's/sample_name_shown/sample_name_to_change/g' *

After that I deleted the sqlite object created by cummeRbund and again created this object using readCufflinks() in R.
This time sample names are changed as desired:
samples(cuff)
sample_index sample_name sample_name parameter value
1            1       Batis                
2            2 Blue_silver                
3            3  Chakwal_50                
4            4      Syn_22


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