hiya, I'm an undergrad who's completely new to bioinformatics and R. I've been assigned a project to analyse the differential gene expression from some Illumina HT-12 v4 data on GenomeStudio but when I try to follow the limma user guide, I run into errors right at the start when I try to use neqc:
x <- read.ilmn(files="Diff Expression Probes.txt", ctrlfiles="Control Probe Profile.txt") y <- neqc(x) Note: inferring mean and variance of negative control probe intensities from the detection p-values. Error in if (alpha <= 0) stop("alpha must be positive") : missing value where TRUE/FALSE needed In addition: Warning message: In min(d) : no non-missing arguments to min; returning InfY<-neqc
I thought maybe I had exported the wrong data from GenomeStudio since the limma user guide says "probe profile.txt" but I only found "Diff. Expression Probes.txt" on GenomeStudio? Or is there some deeper error I haven't noticed? I don't know what it means by alpha either?
Thanks for your help!