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two-color microarray - technical replicates

Hi all,

I am using Limma for the first time to analyze my two-color microarray data. So, I would like to know the best way to proceed to create my Targets file. My experiment has the following technical replicates:

        CY3                                  CY5

1. gene of interest                       control

2. gene of interest                       control

3. control                                     gene of interest

4. control                                     gene of interest

5. gene of interest (treated)         control (treated)

6. gene of interest (treated)          control (treated) 

7. control (treated)                        gene of interest(treated)



.  1=2 / 3=4 / 5=6

My question is: how can I proceed in this part below? 

targets <- cbind(Cy3=c("Gene of interest","Gene of interest", "Control", "Control", "Gene of interest_Treatment", "Gene of interest_Treatment", "Control_Treatment"),  Cy5=c("Control", "Control", "Gene of interest", "Gene of interest", "Control_Treatment", "Control_Treatment", "Gene of interest_Treatment"))

rownames(targets) <- paste("Array",1:7)

parameters <- cbind(C=c(-1,-1, 0, 0, 1, 1, 2), T=c(0, 0, -1, -1, 2 , 2, 1))

rownames(parameters) <- c("Reference","Control","Treatment")  **#  What is the right way to write this part?**                     


modelMatrix(targets, parameters)

modelMatrix(targets, ref="Reference")

design<- model.matrix(targets, parameters)

Thanks in advance

cheers,

Paulo

r microarray software error
• 231 views • link
written by Sanches • Sanches

Read the duplicateCorrelation() help and "11.3 A Correlation Approach to Technical Replication" from limma Users Guide.

• 0 views • link
written by h.mon h.mon

1 answer

Dear genomax,

Thanks for your help.

I have just solved the problem.

Thanks

Best Paulo

• 0 views • link
written by Sanches • Sanches

Please, use ADD COMMENT for these kind of remarks, instead of adding an answer. However, it seems the comment / answer you are thanking is gone? Istvan Albert, genomax, any idea of what is going on? Seems like the second post something like this happens - if I am not mistaken, happened here as well.

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written by h.mon h.mon

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