[BioC] M vs M plots- dye effect in dyeswap exp

[lzarzabal@aol.com]

Hello All,
 
I was wondering if anyone had any suggestions on quality issues with dyeswap slides.  We ran 2 exp's with dye swap slides and some of them looked questionable.  I have attached the M vs M plots.  Also several of the density plots are bimodal.  We had missing spots that were missed by the print tips, which I removed. I read in previous BioC emails that if there is an x pattern on the MvsM plot that it could be due to degradation of the dyes.  The experimenters have assured me that the dyes are not expired and are from a very reputable company.  Does anyone have any ideas, are the slides usable or need to be redone?  We are using in-house RNA.
 
Thanks
LZ