Hello, perhaps I have misunderstood, but I double checked my reagents and Cy5 is the green dye, 532 nm. The LIMMA user's guide (Sept. 22nd, 2004) has Cy3 as green and Cy5 as red. This could adversely effect people using the readTargets and modelMatrix functions it seems. My data seems to be unaffected since I made a design matrix by hand. I assume that in such cases limma calculates M as log2R:G where R is F635 and G is F532, which would be correct. Pardon me if this has been corrected already or if someone else already pointed it out. -Dennis

Dennis, I noticed this on a 'excursion' back to the lab, at first glance confusing. Cy3 DYE is red and Cy5 DYE is blue, they often also have packaging in these colours. However, the adsorption maxima are 532 and 649, and the florescence maxima are 570 and 670 respectively. Therefore, Cy3 is detected as the GREEN CHANNEL and Cy5 the RED CHANNEL. This is further confused as I've seen Cy Dye protein labelling and FISH with Cy3 as the red dye. And I also guess that many people working on data analysis haven't physically seen the dyes. Hopefully, people read the product details and assign sample based on the adsorption laser settings of 532 and 649nm rather than the dye colour, otherwise there may be some interesting mix-ups. HTH, Matt #########original######### >Hello, perhaps I have misunderstood, but I double checked my reagents >and Cy5 is the green dye, 532 nm. The LIMMA user's guide (Sept. 22nd, >2004) has Cy3 as green and Cy5 as red. This could adversely effect >people using the readTargets and modelMatrix functions it seems. My data >seems to be unaffected since I made a design matrix by hand. I assume >that in such cases limma calculates M as log2R:G where R is F635 and G >is F532, which would be correct. Pardon me if this has been corrected >already or if someone else already pointed it out. >-Dennis