I have a problem analysing EPIC arrays with ChAMP. I have a set of 7 arrays - one part of arrays was done during November 2016-January 2017 (4 arrays), second part was done in June 2017.
When I analysed the first and second portion of arrays separately, everything seems ok in both cases, all the samples pass the filtering with Failed CpG fraction around 0.03-0.001.
But when I try to analyse all the arrays together, the filter removes all samples from arrays from June according to great amount of failed probes:
Failed CpG fractionMRK50 BS 0.9194669703 MRK50 oxBS 0.7961700762 Z748 BS 0.8965456313 Z748 oxBS 0.7784871085 TRO63 BS 0.9166965001 TRO63 oxBS 0.7794537127 #etc. for the 3 arrays from June - all the samples were removed by the filter 0568 BS 0.0022115258 0568 oxBS 0.0301945450 0515 BS 0.0014966775 0515 oxBS 0.0195157047 0681 BS 0.0011225081 0681 oxBS 0.0105864528 G89 BS 0.0017611367 G89 oxBS 0.0332179259 #etc. for the other 4 arrays
Also in GenomeStudio the number of probes with detection pval<0.01 was quite similar for all samples.
Any ideas what could be the problem??
I also tried to proceed all the arrays together with minfi but I got an error:
Error in read.metharray(files, extended = extended, verbose = verbose, : [read.metharray] Trying to parse IDAT files with different array size but seemingly all of the same type.
but when I set force=TRUE in
read.metharray.exp(targets = targets, extended = FALSE, recursive = FALSE, verbose = FALSE, force = TRUE)
all the samples were processed without any further problems and the quality control did not show any bad samples.
Unfortunately I don’t know how can I set force=TRUE for read.metharray.exp in ChAMP if I want to do champ.load(method="minfi").
Can anyone help?
Thanks in advance, I will appreciate any answers!!