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

[Wei Shi]

Hi Prasad:

	Have a look at this page: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM614020 . It is clear now they used BeadStudio for the analysis. So probe intensities were firstly subtracted by mean background intensity and then quantile normalized. The data was not log transformed because they are definitely not on the log scale.

	I am not sure if I can answer your previous post about the complex contrast matrix because I am not a statistician. But you can post it again to see if it can be answered by someone else.

Cheers,
Wei


On Apr 8, 2011, at 2:15 PM, Prasad Siddavatam wrote:

> 
> 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
> 
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