What The Meaning Of The Output The Affymetrix Expression Console

Question

[zerohsy]

Hello,I have met the following problems when I handle the .cel DatHeader=[2..26852] EC2003090502AA:CLS=4733 RWS=4733 XIN=3 YIN=3 VE=17 2.0 09/05/03 14:16:05   HG-U133A.1sq 
When I use the expression console,there appears two txt,one is rma.summary.txt.The other is plier-mm.summary.txt.I want to know what the difference of both since I do not fully understand the meaning of the output of the expression console software. Could anyone can tell me what the function of the the expression console software and what meaning of the .cel it is. Thanks a lot!

[Michael]

There must be some documentation to consult first for this commercial software package.

Answer 1

[Michael]

The Expression Console workflow provides the user with a choice of commonly used probe set summarization algorithms. The algorithms offered include: - Robust Multi-array Analysis (RMA) - MAS5 Statistical Algorithm - Probe Logarithmic Intensity Error Estimation (PLIER)

Please read the fine manual.

[zerohsy]

Thanks a lot.And I have the following questions.The .cel I need to handle says " Algorithm=Percentile.AlgorithmParameters=Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004"What does the algorithm means ?And does it mean that the algoritm of the RMA and PLIER is not suitable?Fianlly,how can I handle this .cel?

[Michael]

I think they are related to raw signal extraction and have nothing to do with subsequent normalization.

Fianlly,how can I handle this .cel?

Use Bioconductor/R open source software (e.g. affy package) instead of closed source proprietary software.