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

[Naomi Altman]

If these pairs are dye-swaps, then the M-values should be negatively 
correlated.  In this case, you have a problem (assuming you 
normalized the data first).

If they are not dye-swaps, then perhaps they are OK.  You cannot pay 
too much attention to the smooths outside the main body of the data.

--Naomi

At 11:19 AM 2/6/2006, lzarzabal at aol.com wrote:
>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
>