Entering edit mode
6.4 years ago
ali0jan
•
0
my .CEL raw files are stored in : "C:\Users\Public\Documents\yes\Raw" the CytoScan HD files in : "C:\Users\Public\Documents\yes\Affymetrix\ChAS\Library\CytoScanHD"
I am trying to run the cyto2ATP function on aptParam :
"aptParam <- APTparam(
type="cytoscan",
level="standard",
cel.list="C:/Users/Public/Documents/yes/Raw",
output.path=".",
analysis.path="C:/Users/Public/Documents/yes/Affymetrix/ChAS/Library/CytoScanHD/",
cdf="CytoScanHD_Array.cdf",
chrX="CytoScanHD_Array.chrXprobes",
chrY="CytoScanHD_Array.chrYprobes",
qca="CytoScanHD_Array.r1.qca",
qcc="CytoScanHD_Array.r1.qcc",
snp="CytoScanHD_Array.snplist.txt",
annot.db="CytoScanHD_Array.na32.3.annot.db",
refmodel="CytoScanHD_Array.na32.3.v1.REF_MODEL"
)"
It gives me a warning message:
"running command 'C:/Users/My Pc/Documents/R/win-library/3.4/affy2sv/exec/win64.apt-copynumber-cyto.exe -v 4 --cyto2 false --doDualNormalization true --keep-intermediate-data false --run-geno-qc true --snp-qc-use-contrast true --force true --adapter-type-normalization false --text-output true --cnchp-output false --cychp-output true --set-analysis-name cyhd --analysis loh-segment --analysis cn-neutral-loh --male-gender-ratio-cutoff 1.5 --female-gender-ratio-cutoff 0.9 --xx-cutoff 0.61 --xx-cutoff-high 0.95 --y-cutoff 0.58 --local-gc-background-intensity-adjustment-method none --image-correction-intensity-adjustment-method none --wave-correction-log2ratio-adjustment-method wave-correction-log2ratio-adjustment-method.bandwidth=101.bin-count=25.wave-count=6.wave-smooth=true --cn-calibrate-parameters calibrated-log2ratios.alpha-cn-calibrate=0.564278.alpha-X-cn-calibrate=0.619453.alpha-Y-cn-calibrate=0.494620.beta-cn-calibrate=1.beta-X-cn-calibrate=1.beta-Y-cn-calibrate=1 --analysis genotype... <truncated>"
and does not generate the cyhd.txt files in .apt folder as intended. I am stuck in this problem for a while kindly provide any information you have regarding this issue
Maybe just start with basics like:
output.path="."
)Also, try running it from a shorter file-path. You may have reached a limit for the command line buffer.