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?
I've changed this to a Question rather than Tool, as it is a question about a tool rather than the announcement of a new Tool. Just for future reference.