[BioC] quality assessment and preprocessing for tiling array-based CGH data

[Leon Yee]

Sean Davis wrote:
>> Hi, Sean
>>
>>   Thanks for your advice. However, I have still several questions:
>>
>>   1. The input of dlrs is the log ratios, the log ration extracted from the
>> text file produced by Feature Extraction? or calculated from RGlist -->
>> MAlist ?  I have searched the mailist and seen a post of you mentioned the
>> difference of log ration from Feature Extraction and the default M value
>> from read.maimages.
> 
> You can read the Agilent FE manual for more details, but you can
> probably use either and come to very similar conclusions.  If you use
> the MAlist version, make sure to use only median centering or none for
> normalization.
> 
>>   2. I can get the log ratios of all features including control type of -1
>> and 1, but these features don't have chromosome positions, does this mean I
>> don't need all of them for quality assessment?
> 
> We have not routinely used these probes, no.  If an array fails
> miserably, then these control probes might be useful for determining
> the reason for the failure, though.
> 
>>   3. Some probes with the name of "chr2_random:xxxxx-yyyyyy" will not get a
>> proper mapping on the chromosome, so I should remove these values from the
>> input of dlrs. Is it so?
> 
> You can either remove them or treat chr2_random as a separate chromosome.
> 
>>   4. How could I handle those 1000 probes repeating 3 times?  They will be
>> mapped on the same chromosome position by three per group.
> 
> You could choose one at random or use a mean or median of them.  My
> guess is that they agree very closely with one another so the choice
> should not affect the results much.

Hi, Sean

     Thank you very much for your detailed reply and help.

     Where can I get the references or official documentations about 
dlrs method?

     In addition, we have design our array with dye-swap [test-cy3 vs 
ref-cy5, and test-cy5 vs ref-cy3]. Is there any method for utilizing the 
information here for quality assessment?

Best wishes!
Leon