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meffil.qc.summary Error and Warning #56
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Sorry to hear about this error. Could you run the following code and send me the output generated? outlier.sd <- 3
dat <- data.frame(
sample.name = sapply(qc.objects, function(x) x$sample.name),
methylated = sapply(qc.objects, function(x) x$median.m.signal),
unmethylated = sapply(qc.objects, function(x) x$median.u.signal),
stringsAsFactors=F
)
fit <- lm(methylated ~ unmethylated, dat)
dat$resids <- residuals(fit)
dat$methylated.lm <- predict(fit)
interval.size <- outlier.sd*sd(dat$resids)
dat$upper.lm <- dat$methylated.lm + interval.size
dat$lower.lm <- dat$methylated.lm - interval.size
dat$outliers <- (dat$resids > mean(dat$resids) + interval.size
| dat$resids < mean(dat$resids) - interval.size)
na.idx <- which(is.na(dat$outliers))
cat(nrow(dat), length(na.idx), "\n")
if (na.idx > 3) na.idx <- na.idx[1:3]
print(dat[na.idx,]) |
Hi, Here is the output `cat(nrow(dat), length(na.idx), "\n")
Thanks in advances, Rossella |
Ah I see. The qc.summary() is failing when it attempts to identify outliers because only one sample is being analysed. Although some quality information can be generated for a single sample, variation between samples is necessary to evaluate technical variation. Do you have more samples? Will you regularly need a QC procedure to apply to individual samples? |
Thank you so much for your support. That was the issue. |
Hi all,
I have recently experiend the following error using meffil.qc.summary on EPICv2 array
qc.summary <- meffil.qc.summary(qc.objects,verbose=TRUE)
[meffil.qc.summary] Fri Dec 15 14:04:36 2023 Sex summary TRUE
[meffil.qc.summary] Fri Dec 15 14:04:36 2023 Meth vs unmeth summary
Error in if (any(dat$outliers)) p1 <- p1 + geom_point(data = subset(dat, :
missing value where TRUE/FALSE needed
In addition: Warning message:
The
<scale>
argument ofguides()
cannot beFALSE
. Use "none" instead as of ggplot2 3.3.4.ℹ The deprecated feature was likely used in the meffil package.
Please report the issue to the authors.
This warning is displayed once every 8 hours.
Call
lifecycle::last_lifecycle_warnings()
to see where this warning was generated.Any help would be very appreciated.
Thank you
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