head(coriell)
       Clone Chromosome Position Coriell.05296 Coriell.13330
    1  GS1-232B23          1        0            NA      0.207470
    2  RP11-82d16          1      468      0.008824      0.063076
    3  RP11-62m23          1     2241     -0.000890      0.123881
    4  RP11-60j11          1     4504      0.075875      0.154343
    5 RP11-111O05          1     5440      0.017303     -0.043890
    6  RP11-51b04          1     7000     -0.006770      0.094144

What is the value for the column Coriell.05296 and Coriell.13330? It is log2ratio of copy number or log2R ratio or normalized intensity value?

DNAcopy manual shows they are log2ratio for two cell lines. This is a very vague explanation.

It looks like log2 of copy number.

This is the PennCNV output.

chr20:50048779-50243701       numsnp=104    length=194,923     state2,cn=1 ./signalfile/gw6.GSM917310_MT643_MDT startsnp=CN_212439 endsnp=CN_892457
chr20:51678976-51775770       numsnp=73     length=96,795      state2,cn=4 ./signalfile/gw6.GSM917310_MT643_MDT startsnp=SNP_A-1851231 endsnp=CN_901307
chr20:51989590-52036398       numsnp=34     length=46,809      state2,cn=1 ./signalfile/gw6.GSM917310_MT643_MDT startsnp=CN_903443 endsnp=SNP_A-1875628

This is birdsuite output.

sample  sample_index    copy_number chr start   end per_probe_score size    num_probes  lod_score
GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A01_31218.CEL 1   2   1   51598   16217842    8245    16166244    8245    8245
GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A01_31218.CEL 1   3   1   16236527    16241564    62.82   5037    4   7.19
GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A01_31218.CEL 1   2   1   16246917    16808594    19.85   561677  233 302.38

If I used copy number as input of DNAcopy, they are cn=<value> in PennCNV and copy_number column in birdsuite. So, the possible value will be log0, log1=0, log3=1.58, log4=2.

But is DNAcopy coriell data, they have 0.207470, 0.123881,0.063076. None of these equle to above values. How can they get these values?