No, FITS files and CR2 files of Canon cameras contain exactly the same raw image data. The only difference is that these data are scaled in FITS files, so you cannot use FITS and CR2 mixed for one project, but scaling does not change the quality.
However, FITS files contain a lot of useful metadata which are absent in the CR2 files.
Yes, i am newbie here.i discoverd that for DSLR it looks like its not handy to save your images to fits. when you stack them the fit have huge amount of noise and lines while CR2 in my case looks smooth. lost of time this weekend.
As I wrote before: you have to use ALL files (lights and calibration files) in the same format: either in FITS or in CR2 format. When you mix the formats, the calibration will produce wrong results.
i my case i did, i used bias/dark/flat/lights fits from sgp, i used the bayer files generated via pixinsight to stack. So i dont understand the noise in the picture compared to the CR2 stack which is more smooth.
Any hints on this?
I think this is off-topic here and would be better discussed in the PI forum. The information that was given so far by you is too poor, anyway I cannot conclude from these informations what went wrong.
I used a Canon DSLR myself (EOS 600D = Rebel T3i) and used CR2 format at first and later on FITS, both saved by SGP. So I know that it works well when the calibration is carried out in the right way.