[BioC] avereps function in limma (dealing with negative values in illumina)

[Prasad Siddavatam]

Wei Shi <shi at ...> writes:

> 
> Hi Prasad:
> 
> 	I had a close look at one of the datasets:
> http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?
view=data&acc=GSM614020&id=15413&db=GeoDb_blob51
> . The header information in this page is:
> 
> #ID_REF = 
> #VALUE = Quantile, subtract background
> #1690411024_A.Detection Pval = 
> 
> It looks like they performed quantile normalization to the data but also 
subtracted probe intensities by
> the background intensity. The negative values in the table seemed to result 
from the "subtract
> background" step. However, it is unclear how the data was analyzed at all. 
> 
> I would suggest you to contact the authors who generated these data. This 
might be the easiest and quickest
> way to get around this issue and get the data you want.
> 
> Hope this helps.
> 
> Cheers,
> Wei


Dear Wei, 

Thank you very much for the information. Do you think the data is log2 
transformed? I can't transform because of negative values (My original problem).

Can you please answer my question I posted today with subject "limma
complex contrast matrix" on 011-04-07 17:05:59 GMT


Prasad