We have found that automatic cosmic ray rejection in extraction of a spectrum from a 2-D image can change the equivalent width of some lines. We recommend using uncleaned spectra for equivalent widths in such situations. That would be the second spectrum in IRAF multispec files which have been cleaned, the third being the background which was removed, and the fourth being the raw extracted spectrum.
[rvsao]
[xcsao]
[emsao]
[sumspec]
[linespec]
[eqwidth]