I measured the OD of my samples using spectrophotometer (750 nm), and microplate reader, and there was a difference between them.. so when do I consider the difference a minor and neglectable.. and what could be wrong?
First of all, the optical path length in the spectrophotometer and in the microplate reader is probably not the same: it is fixed in the spectrophotometer and depends on the depth of the liquid in the microplate reader. Furthermore, if you are measuring OD (i.e. turbidity) and not absorbance, the reading will depend on the geometry of the device, since OD actually measures the fraction of light that gets deflected away from the path leading to the photodetector. Thus you should determine using the same sample the proportionality factor for the conversion between the spectrophotometer and the microplate reader.
Absorbance readings on optical devices are affected by the reflection, dispersion, and bypass of the incident light. In general, one expects these properties to be superior in standard cells mounted in a spectrophotometer; however, if it's simply comparisons you need does that matter?
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