At 11:00 AM 13/01/2006, Matthew Scholz wrote:
>Gordon,
>
>Thank you for your thoughtful reply. I apologize for not having
>provided a more thorough accounting of my R session. To save space,
>I have left out the output of the initial steps (reading in the
>files, kooperberg correcting them, and quantile normalizing), but
>would be happy to provide them if you think they would be of use. I
>have, nonetheless, included the code I inputted to generate the data
>object RGAn that I pass to the lmFit function.
[snip]
> > designmatrix <- modelMatrix(targetsA, ref="RC")
>Found unique target names:
> A B C D E RC
> > designmatrix
> A B C D E
>2005-11-18_A130high -1 1 0 0 0
>2005-11-16_A121high 0 -1 1 0 0
>2005-11-15_A117high 0 0 -1 1 0
>2005-11-16_A119high 0 0 0 -1 1
>2005-11-17_A127high 0 0 0 0 -1
>2005-11-17_A128high 1 0 0 0 0
>2005-11-17_A129high -1 0 1 0 0
>2005-11-18_A131high 0 -1 0 1 0
>2005-11-16_A120high 0 0 -1 0 1
>2005-11-15_A118high 0 0 0 -1 0
>2005-11-22_A137high 1 0 0 0 -1
>2005-11-18_A136high 0 1 0 0 0
> > designfitA <- lmFit(RGAn, design=designmatrix, method="ls")
> > designfitA <- eBayes(designfitA)
>
>#And here's a look at a subset of the data object with the warning
>that I am asking about
>
> > designfitA[2,1]
>An object of class "MArrayLM"
>$coefficients
> A
>[1,] 0.07587446
>
>$stdev.unscaled
> A
>[1,] 0.7007649
>
>$sigma
>[1] 2.338142
>
>$df.residual
>[1] 6
>
>$cov.coefficients
> [,1]
>[1,] 0.4166667
>
>$pivot
>[1] 1 2 3 4 5
>
>$method
>[1] "ls"
>
>$design
> A B C D E
>2005-11-18_A130high -1 1 0 0 0
>
>$genes
> Block Row Column ID Name
>2 1 1 2 MZ00040730 TC245883
>
>$Amean
>[1] 6.35853
>
>$df.prior
>[1] 3.102594
>
>$s2.prior
>[1] 0.5266471
>
>$var.prior
>[1] 0.5289733
>
>$proportion
>[1] 0.01
>
>$s2.post
>[1] 3.783035
>
>$t
> A
>[1,] 0.05566768
>
>$p.value
> A
>[1,] 0.9568093
>
>$lods
> A
>[1,] -4.959734
>
>$F
>[1] 0.3347732
>
>$F.p.value
>[1] 0.879682
>
>Warning message:
>design matrix is singular
>
>Thanks again,
>
>Matt
Thanks for providing the detailed session. This clarifies things.
The warning message is not actually contained in the fitted model
object. If you type
designfitA
at the R prompt, you won't see any warning message. The warning
message is generated and written to the screen by the subsetting
operation. If you typed
fitsubset <- designfitA[2,1]
you would see the warning while if you type
fitsubset
you won't. What you're seeing in the output from your session is the
contents of fitsubset followed by the warning message. The warning
message may appear to be part of the object just because it follows
immediately in the output.
The subset designfitA[2,1] means the model fit for just the second
gene and the first coefficient. (Why do you want this?) The design
matrix is stored as part of the fitted model object, and the
subsetting operation changes it as well. The warning message is
intended to warn you that the subsetted design matrix stored in
fitsubset should not be used as input for any subsequent linear model
fits. I agree that the warning is unexpected in this situation, and I
am going to change it. (In fact I'm going to change the way in which
subsetting affects the design matrix.)
The thing to remember is that your linear model fit was perfectly
correct and you should be confident about using it. The warning
message occured when, later on, an operation was used which changed
the copy of the design matrix which was stored in the fitted model
object. The warning doesn't relate to the design matrix used to fit
your linear model. Rather it refers to a different and smaller design
matrix produced when you subsetted the fitted model object.
Best wishes
Gordon
