Change sample names while using cummeRbund 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        &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;


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:

&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;-"


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?
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        &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;