
Hello, I have a question. I'm Working with one-color microarrays . I worked in 4 conditions different and each condition I have 4 replicates. Now, my question is  when I load the files to Bioconductor, I load as follows:
 my.filenames <- c ("Condic1_repl1.txt",
                                 "Condic1_repl2.txt",
                                 "Condic1_repl3.txt",
                                "Condic1_repl4.txt",
                                 "Condic2_repl1.txt",
                                 "Condic2_repl2.txt",
                                "Condic2_repl3.txt",
                                 "Condic2_repl4.txt",
                                 "Condic3_repl1.txt"
                                "Condic3_repl2.txt",
                                 "Condic3_repl3.txt",
                                 "Condic3_repl4.txt",
                                 "Condic3_repl1.txt",
                                "Condic3_repl2.txt",
                                 "Condic3_repl3.txt",
                                 "Condic3_repl4.txt")

Subsequently, I realize the normalization procedure and some statistical calculations:
 one.col1 <-list (R = "gMeanSignal" G = "gProcessedSignal"
            Rb = "gBGMedianSignal", Gb = "gProcessedBackground")
 RG1 <- read.maimages (my.filenames, source = "agilent", columns = one.col1, dec =".")
  RG1 <- backgroundCorrect (RG1, method = "half", offset = 50)
  MA1 <- normalizeBetweenArrays (RG1, method = "quantile")
 fit1 <- lmFit (MA1, design = NULL)
 fit1 <- eBay (fit1)

But my question is: how I can specify to bioconductor which files correspond to Control, or which correspond to microarrays with  treatment?

Regards, Paz
 		 	   		  
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