[BioC] Technical Replicates in EdgeR

[Ryan C. Thompson]

Hi there,

No, there is absolutely no problem with dropping a lane of data if you 
believe that lane to have technical issues. I would recommend that you 
use the plotMDS function to verify that the counts in the bad lane are 
indeed different from the other two lanes.

-Ryan

On Fri 21 Mar 2014 01:45:51 PM PDT, Neha Mehta wrote:
> Hello,
>
> I am a graduate student and fairly new to RNA-Seq. In my study I have a 2x2
> design with each group containing 4 bio reps and each bio rep has 3
> technical replicates (same library prep, but each sample is processed in 3
> different lanes). After studying my frequency count data I have found that
> the count data in lane 1 is very different from lane 2 and 3 for most to
> all bio samples. I plan to use EdgeR for DE analysis and I am wondering if
> it is OK to sum count totals from just lanes 2 and 3. All documentation I
> have read states that technical variation is small so you should sum all
> tech reps, but in this case it seems I have noticed greater variation in
> one lane and therefore it does not make sense to include it. I have not
> found any reason why you can not just sum 2 out of 3 technical replicates
> if you know that one technical replicate has much higher variation than the
> other two. Please let me know if you have any evidence for this.
>
> Thank you very much in advance.
>