[BioC] Limma: Error in backsolve
naomi at stat.psu.edu
Mon Jan 2 23:07:56 CET 2006
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.
At 01:29 PM 1/2/2006, Gerhard Thallinger wrote:
> 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 =
>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
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
Naomi S. Altman 814-865-3791 (voice)
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348 (Statistics)
University Park, PA 16802-2111
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