[BioC] Is it possible to read in Bluefuse and Agilent files together using read.maimages() function in limma?

[Gordon K Smyth]

Dear Parisa,

I've never tried to normalize together intensity data from different image 
analysis programs.  Even if the microarray platforms were the same in both 
cases, I would view that as a risky procedure.  If you were to attempt it, 
you would need to attend very carefully to batch correction between the 
platforms as part of the downstream analysis.

If you are processing Agilent data, please follow the case study in the 
limma User's Guide that deals with single-channel Agilent data.  It is 
Section 11.8 titled "Agilent Single-Channel Data: Gene expression in 
thymus from female Wistar rats".

Best wishes
Gordon

On Fri, 1 Jun 2012, Parisa Razaz wrote:

> Hi,
>
> Thanks for getting back to me.
>
> If I read the two file types in separately, would it be possible to then 
> normalise and analyse the data together (after merging)? I am hoping to 
> follow a protocol similar to that outlined here: 
> http://matticklab.com/index.php?title=Single_channel_analysis_of_Agilent_microarray_data_with_Limma
>
> Thanks,
>
> Parisa
>
>
> On 1 Jun 2012, at 11:19, Gordon K Smyth wrote:
>
> No, it can't combine any two types.  Read them in instead using separate
> calls to read.maimages().
>
> Gordon
>
> On Fri, 1 Jun 2012, Parisa Razaz wrote:
>
> Hi,
>
> Is it possible to read in both Bluefuse and Agilent files together using the read.maimages() function in limma?
>
> Thanks,
> Parisa

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