[BioC] MAS5 and GCOC difference to get CEL files

[James W. MacDonald]

Adaikalavan Ramasamy wrote:
> I assume that you used 
>  i)  12 CEL files to obtain MAS 5.0 via R and
>  ii) 4 CEL files via GCOS (GeneSpring Operating Software ?) which I
> assume also gives MAS 5.0

GCOS stands for GeneChip Operating Software, and is the Affymetrix 
replacement for MAS5.

> On Mon, 2004-09-13 at 10:41, Delphine Fleury wrote:
> 
>>Dear all,
>>I am analyzing affymetrix data ATH1 from the same biological experiment 
>>(material growth, harvesting and RNA extraction done at the same time in 
>>the same conditions) but hybridized at 2 different dates (the 2d set 
>>done 1 year later). So , 12 chips were preprocessed with MAS5 getting 
>>CEL files and 4 chips with GCOS.
>>At first, I see that the size of the CEL files are about 11 MB for the 
>>12 chips and about 5 MB for the 4 last chips. 

The 12 files are in the old-style text format, whereas the 4 newer files 
are in binary format, and hence are smaller.

Secondly, the mean signal
>>of the 4 last chips is lower than those from the 12 chips (cf boxplots 
>>before normalization, and AffyPLM). 
>>Is it possible that the lower signal is related to the preprocessing 
>>method from GCOS ?

Possible, but not likely. You should check with whoever did the 
processing and see if they used the ENZO kit or the new IVT kit from 
Affy with the last four chips. I am betting that they switched to the 
new IVT kit. If so, this is probably very bad news, because I don't 
think the results will be comparable. I know for a fact that RMA, GCRMA, 
and MAS5 will not give comparable results for the two IVT protocols. For 
the next month or two you can still get the ENZO kit, so if you need 
data from the other four chips I would recommend re-doing them with the 
ENZO kit.

>>Is there someone who observe the same things ?
>>Could it be a problem to analyse all chips together ?
>>Thanks
>>Delphine
>>
> 
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor


-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109