Hi all,

 

I am extremely new at R and microarray analysis and so some of my questions 

may sound silly but I do hope someone will be able to help.

 

I am analyzing Agilent one colour custom 4x44k array data. My targets file
is 

labelled as:

FileName    Cy3

1           control1

2           control1

3           mutant1

4           mutant2

5           control1

6           control2

7           mutant1

8           mutant2

where I have 3 technical replicates and 2 biological replicates of my
control, 

2 biolrep of mutant 1 and 2 biolrep of mutant 2. i.e.

 

As such how do I define my design matrix? Secondly how do I convert my data
to 

an exprSet object so that I can analyse it like a Affymetrix array?

 

As a sidenote, I have already created my MA object and tried to fit it as:

> fit<-lmFit(MA)

> fit<-eBayes(fit)

But I get an error:

Error in if (evar > 0) { : missing value where TRUE/FALSE needed

In addition: Warning message:

In fitFDist(var, df1 = df) :

  More than half of residual variances are exactly zero: eBayes unreliable

 

Any idea what was wrong with my data? I am sure this is some silly
formatting 

error that i must have missed out.

 

Thank you in advance.

 

Cheers

Wendy


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