Question: cyto2ATP do not generate cyhd.text files of .CEL
0
gravatar for ali0jan
12 months ago by
ali0jan0
ali0jan0 wrote:

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

assembly snp R • 473 views
ADD COMMENTlink modified 10 months ago by Biostar ♦♦ 20 • written 12 months ago by ali0jan0

Maybe just start with basics like:

  • ensuring that you have write access to the directory where it's attempting to create the file
  • ensuring that it has not created the file elsewhere (you specify output.path=".")
  • ensuring that the function can tolerate spaces in your path

Also, try running it from a shorter file-path. You may have reached a limit for the command line buffer.

ADD REPLYlink modified 12 months ago • written 12 months ago by Kevin Blighe32k
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