Generally the Qubit is considered less variable then the bioanalyzer. However, if both are run properly, they are generally quite similar (+/- 10%). Do you have your bioanalyzer traces that you could show?

Bioanalyzer traces can be skewed by overloading, poor priming, improper ladder dilution, poor pipetting technique, etc. They are generally more sensitive to human error. 

Errors in Qubit may be due to temperature fluctuations during readings, or poor standard preparation. 

Therefore, as Qubit is generally less sensitive to error I would say to go with the Qubit or to post your electropherograms so that we may be able to see if there are any notable issues with the traces.

Hi Michael, many thanks for your reply. I've attached the electropherograms for reference. Please ignore the last two samples..

Hi Qui,

It looks like you put a lot of RNA into the pico chips. The recommended input for quantification is less than 5 ng/microliter. In the future, you should do a serial dilution until your sample is under 5 ng/microliter. This will make quantification more accurate, because as you can see, the marker is much much smaller than your RNA peaks. This makes the comparison between the two more variable. You may also consider using nano chips instead of pico chips. They are a little bit cheaper, you can load more samples in each chip, and you won't need to dilute. 

It may be my imagination, but it also looks like there may be some smearing above the 28S peak, suggesting that perhaps there is some DNA contamination. If this were the case, the bioanalyzer would consider this as RNA, but the Qubit, as it is specific to RNA, would not. You may want to check for DNA contamination.

Hope this helps!

Hi Michael, the reason why we used the pico chip is because of the ultra low Qubit reading we first got.. Hence we were rather surprised by the results from Bioanalyzer... Guess I have to re-analyse it on the nano chip.. And thanks for pointing out the potential DNA contamination :) will get that checked! this is really helpful! cheers

Hi Michael,

I have been using Pico Chips of the Agilent Bioanalyser. I have got reads of 29pg/ul of RNA after extracting miRNA with Qiagen's miRNeasy kit from plasma. Would I get similar results in the Qubit? I can't find many papers about comparing results of a Bioanalyser and Qubit. Any help would be appreciated! Thanks!

Hi everyone, 

Thanks for the answers Michael. Similarly, I used the HS RNA Qubit assay and later sent the samples for bioanalysis. The concentrations never differed with 10%, more like 55-365%. I'm not blaming anyone, for all I know I could have been the greatest error. :) With my lower concentration samples (5-16ng/ul from Qubit) the concentrations were more often lower in the Bioanalizer (6/9 samples). The low/moderate concentration samples (15-35ng/ul from Qubit) were all higher in the Bioanalizer (10 samples). As the concentrations increased so the difference between the two methods increased, hence 365% for a sample that was 29.6ng/ul in the Qubit and 108ng/ul in the Bioanalyzer. I'll use the Bioanalizer concentrations for cDNA synthesis. Any comments? 

Hope this will help someone.

I have had the same problem recently using picogreen and the bioanalyzer, where the bioanalyzer almost consistently doubled the concentration measured by the fluorescent nanodrop. Generally, I use fluorescent results to determine concentration, and use the bioanalyzer to determine quality. It would be an interesting experiment to take something of a known concentration (RNA standards) and compare their concentration on both kits.

Great getting some confirmation on that, thanks Michael. It would be interesting to compare. I would love to see the difference.