Hi ,

I am running our 450K data under methylumi module for QC but facing
following issue:

samplefile <- "./analysis/samples_original"
datafile <- "./analysis/inf_meth_pval_data.txt"
samples <- read.table(samplefile, header=TRUE, sep="\t")
meth <- methylumiR(datafile, sampleDescriptions=samples)
--------Error in grep(dattypes$original[i], cn) : invalid 'pattern' argument

####Is this a memory error or I am doing something wrong.######

following are the columns I have in the files:
Sample file:
SampleID SampleLabel Gender Type

dataFile:
TargetID ProbeID_A ProbeID_B C1.AVG_Beta C1.Avg_NBEADS_A C1.Avg_NBEADS_B
C1.BEAD_STDERR_A C1.BEAD_STDERR_B C1.Signal_A C1.Signal_B C1.Detection Pval
C1.Intensity C2.AVG_Beta C2.Avg_NBEADS_A C2.Avg_NBEADS_B C2.BEAD_STDERR_A
C2.BEAD_STDERR_B C2.Signal_A C2.Signal_B C2.Detection Pval C2.Intensity
C3.AVG_Beta C3.Avg_NBEADS_A C3.Avg_NBEADS_B C3.BEAD_STDERR_A
C3.BEAD_STDERR_B C3.Signal_A C3.Signal_B C3.Detection Pval C3.Intensity
C4.AVG_Beta C4.Avg_NBEADS_A C4.Avg_NBEADS_B C4.BEAD_STDERR_A
C4.BEAD_STDERR_B C4.Signal_A C4.Signal_B C4.Detection Pval C4.Intensity
C5.AVG_Beta C5.Avg_NBEADS_A C5.Avg_NBEADS_B C5.BEAD_STDERR_A
C5.BEAD_STDERR_B C5.Signal_A C5.Signal_B C5.Detection Pval C5.Intensity
C6.AVG_Beta C6.Avg_NBEADS_A C6.Avg_NBEADS_B C6.BEAD_STDERR_A
C6.BEAD_STDERR_B C6.Signal_A C6.Signal_B C6.Detection Pval C6.Intensity
C7.AVG_Beta C7.Avg_NBEADS_A C7.Avg_NBEADS_B C7.BEAD_STDERR_A
C7.BEAD_STDERR_B C7.Signal_A C7.Signal_B C7.Detection Pval C7.Intensity
C8.AVG_Beta C8.Avg_NBEADS_A C8.Avg_NBEADS_B C8.BEAD_STDERR_A
C8.BEAD_STDERR_B C8.Signal_A C8.Signal_B C8.Detection Pval C8.Intensity
C9.AVG_Beta C9.Avg_NBEADS_A C9.Avg_NBEADS_B C9.BEAD_STDERR_A
C9.BEAD_STDERR_B C9.Signal_A C9.Signal_B C9.Detection Pval C9.Intensity
C10.AVG_Beta C10.Avg_NBEADS_A C10.Avg_NBEADS_B C10.BEAD_STDERR_A
C10.BEAD_STDERR_B C10.Signal_A C10.Signal_B C10.Detection Pval C10.Intensity
C11.AVG_Beta C11.Avg_NBEADS_A C11.Avg_NBEADS_B C11.BEAD_STDERR_A
C11.BEAD_STDERR_B C11.Signal_A C11.Signal_B C11.Detection Pval C11.Intensity
C12.AVG_Beta C12.Avg_NBEADS_A C12.Avg_NBEADS_B C12.BEAD_STDERR_A
C12.BEAD_STDERR_B C12.Signal_A C12.Signal_B C12.Detection Pval C12.Intensity
ILMNID NAME ADDRESSA_ID ALLELEA_PROBESEQ ADDRESSB_ID ALLELEB_PROBESEQ
INFINIUM_DESIGN_TYPE NEXT_BASE COLOR_CHANNEL FORWARD_SEQUENCE GENOME_BUILD
CHR MAPINFO SOURCESEQ CHROMOSOME_36 COORDINATE_36 STRAND PROBE_SNPS
PROBE_SNPS_10 RANDOM_LOCI METHYL27_LOCI UCSC_REFGENE_NAME
UCSC_REFGENE_ACCESSION UCSC_REFGENE_GROUP UCSC_CPG_ISLANDS_NAME
RELATION_TO_UCSC_CPG_ISLAND PHANTOM DMR ENHANCER HMM_ISLAND
REGULATORY_FEATURE_NAME REGULATORY_FEATURE_GROUP DHS Index


Thanks for your help.

Shruti

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