Error when using limma contrasts.fit
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Adam Witney ▴ 10
@adam-witney-1381
Last seen 9.6 years ago
Hi, I am going through the limma User Guide and am having a problem using contrasts.fit for my data. I have three biological replicates, two of which have duplicate arrays and one has triplicate arrays. I have a targets file like so: SlideNumber FileName Cy3 Cy5 A1 File1 wt1 mu1 A2 File2 mu1 wt1 B1 File3 mu2 wt2 B2 File4 wt2 mu2 C1 File5 mu3 wt3 C2 File6 mu3 wt3 C3 File7 wt3 mu3 I am simply trying to follow userguide section 11.2, but am having problems: > design <- modelMatrix(targets, ref="wt1") Found unique target names: mu1 mu2 mu3 wt1 wt2 wt3 > design <- cbind(Dye=1, design) > colnames(design) [1] "Dye" "mu1" "mu2" "mu3" "wt2" "wt3" > fit <- lmFit(MA, design) Coefficients not estimable: wt2 wt3 > cont.matrix <- makeContrasts(MUvsWT=(mu1+mu2+mu3-wt2-wt3)/3, levels=design) > fit2 <- contrasts.fit(fit, cont.matrix) Error in contrasts.fit(fit, cont.matrix) : trying to take contrast of non-estimable coefficient Am I doing this correctly? Also I noticed that the userguide refers to designMatrix() which I believe has been deprecated in favour of modelMatrix(), should this have been changed in the userguide? (R-2.1.1, limma 2.0.5, MacOSX 10.3.9) Thanks for any help Adam -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
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