danny92:
If I need to sample two channels at 1 kHz, I have to set the sampling rate at 2 kHz?
that's right.
Don't Serial.print inside the interrupt handler.
If you read ADC_LCDR in the interrupt handler, set only DRDY bit in ADC_IER because reading ADC_LCDR will not clear EOC bit (the datasheet page 1322 is wrong !)