[BioC] Limma: Error in backsolve

[Naomi Altman]

The problem is that in your design you have no biological 
replicates.  If you use blocks, then you must have blockwise 
replication.  You have no d.f. for testing.

--Naomi

At 01:29 PM 1/2/2006, Gerhard Thallinger wrote:
>Dear all,
>
>   I am analyzing an experiment consisting of 4 one-channel
>hybridizations with two conditions and a technical replicate
>for each of them. I am using limma 2.4.4 (2005/11/29) under
>R 2.2.0 on Windows. The design matrix is as follows:
>
>    0h  2h
>1   1   0
>2   1   0
>3   0   1
>4   0   1
>
>Since there are technical replicates the correlation between them
>should be taken into account:
>
>   techrep <- c(1,1,2,2)
>   corfit <- duplicateCorrelation(signal(anaexp), ndups = 1, block = techrep)
>   fit <- lmFit(signal(anaexp), design, block = techrep, cor = 
> corfit$consenus)
>
>The fit aborts with the following error:
>   Error in backsolve(cholV, y, transpose = TRUE) :
>          NA/NaN/Inf in foreign function call (arg 1)
>   In addition: Warning messages:
>   1: NaNs produced in: sqrt(dfitted.values)
>   2: NaNs produced in: sqrt(dfitted.values)
>
>The error is probably a consequence of the warnings from the "corfit <-" step.
>What value would one expect for the consensus correlation ?
>Any ideas how to work around these error ?
>
>The fit without block and cor works flawlessly. Trying to define contrasts
>I encountered the following error messages:
>
>   cont <- makeContrasts("2h-0h", levels = design)
>   Error in parse(file, n, text, prompt) : syntax error in "2h"
>
>Obviously a digit as the first character is not allowed. Prepending a "T"
>before the condition solved this problem. Using a variable for the contrast
>lead to a different message:
>
>   ctr <- "T2h-T0h"
>   cont <- makeContrasts(ctr, levels = design)
>   Error in eval(expr, envir, enclos) : object "ctr" not found
>
>This could be circumvented by using the following construct:
>
>   cmd <- paste("cont <- makeContrasts(", ctr, ", levels = design)", 
> sep = '"')
>   eval(parse(text = cmd))
>
>TIA for your help
>
>Gerhard
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111