This is a very common error and it's often fixable. I'm attaching an example of what the DNA 1000 ladder is supposed to look like. Would you be able to take a screenshot of yours and upload it? It's much easier to help with these problems if I can see what the exact issue is :)

The most common cause of this error is a random spike occurring and being misidentified as a ladder peak or a marker, resulting in the instrument not seeing the expected number of peaks and freaking out. Alternatively, if the ladder is old or degraded or the chip was set up incorrectly, the height of the peaks can be lower than expected causing some or all of them not to be automatically detected. These problems can both be fixed by using manual integration mode: go into the 'Peak Table' view and right-click on the display and select 'Manual Integration', which will allow you to manually set the markers and peaks. Because the ladder peak intensity is used for quantification, you should not trust the quant result from a run affected by this problem - but if you can clearly identify each of the peaks which is supposed to be there and correctly set them in the software, then you can still use the sizing information from this run.

Other possible causes of runs where the samples look fine but the ladder failed are that the ladder isn't present (you forgot to load it or put it in the wrong well), the baseline is disturbed (usually caused by salt or organic contamination of samples) or the ladder tube has been contaminated with other DNA. These problems can only be fixed by repeating the run. A screenshot would really help with diagnosis :)

Hi Laura Leighton thank you so much for your answer. This is the picture's gel. I haven't the standard curve.. Also I haven't the ladder's electropherogram

This is an example of the curve samples Laura Leighton

Larissa do R. B. Matos

Ok, so there's definitely been a problem with detection of your ladder bands. The instrument can only create the standard curve and show the sizing scale if it is able to correctly interpret the ladder, so that's why those features are missing right now. The first thing to check is that all the bands are present. 11 ladder fragments + upper marker + lower marker = 13, and we can see 13 bands in your ladder which are similar in intensity, and which seem to be spaced the same as mine - so your ladder has run ok, but has not been interpreted correctly by the software. On your ladder, the upper marker is not detected, and the second band is incorrectly identified as the lower marker. You should be able to fix this in the Peak Table tab (right click on the top of the marker peak to get the option to manually set upper/lower marker). I think that if you manually set the lower and upper marker, the software should autodetect the rest of the ladder peaks, but if it doesn't, you can use manual integration mode to tell it where the ladder peaks are (right click anywhere in the sample area and select manual integration.)

The next thing needs to be fixed to get sizing information is that your upper and lower markers for your samples have not been correctly detected. The software detected a lower marker in sample 4 (green band) and an upper marker in sample 5 (purple band) but neither is correct and the other samples all have no markers detected at all. But looking at the image, you can see that the markers are actually there: in every sample there is a band at the bottom and a band at the top that approximately match the smallest and largest bands visible in the ladder well. So you can use peak table to manually set upper and lower marker in every sample. If the red dots above each sample on the simulated gel go away after these issues are fixed, then you should be able to use the sizing information from this run. If that's all you need from it, then hopefully problem solved :)

There are a few other issues with the run that I thought I'd mention. There is a dip below baseline in your sample - I labelled it so you can see what I mean. Looking at your gel, I can see that it is in all of the samples where the strong amplicon is present (1-4 and 8-12). I have seen this happen when samples are too concentrated or when they contain something (salt or detergent usually) that the instrument doesn't like. Diluting the samples and running them again might help with both these problems. I also noticed that your scale in fluorescent units is low: on my DNA 1000 runs, the lower marker usually comes up at around 100FU, but in yours it's around 5. Is it possible your reagents are very expired, or have been handled incorrectly (left out of the fridge, exposed to light, etc?) This doesn't invalidate your run but it does reduce your signal:noise ratio (see how the background is quite grey? It should be white) so if you can find the issue and fix it, you will probably get better results in the future :)

Sorry this got so long - I hope it is helpful :)