Kun:LabNotes/ASE/2008-2-1: Difference between revisions
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(New page: ==Data analysis of recent Solexa runs== {| {{table}} | align="center" style="background:#f0f0f0;"|'''ID''' | align="center" style="background:#f0f0f0;"|'''Agilent Lib''' | align="center" s...) |
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==Data analysis of recent Solexa runs== | ==Data analysis of recent Solexa runs== | ||
===Criteria for ASE=== | |||
#1 Heterozygous SNPs: gDNA MAF < 0.15 (false positive rate=8/541=1.5%) | |||
#2 cDNA MAF<0.4; | |||
#3 Chi-square > 6.64 (p=0.01, df =1); | |||
#4 Three categories: | |||
*Balanced; | |||
*Imbalanced; | |||
*Uncertain; | |||
#5 Three level ofs confidence | |||
*Consistent: at least two SNPs with the consistent pattern. | |||
*Probably: only one SNPs in a gene. | |||
*Conflicting: two or more SNPs showing conflicting patterns. | |||
===Summary of Solexa runs=== | |||
{| {{table}} | {| {{table}} | ||
| align="center" style="background:#f0f0f0;"|'''ID''' | | align="center" style="background:#f0f0f0;"|'''ID''' |
Revision as of 18:27, 2 February 2008
Data analysis of recent Solexa runs
Criteria for ASE
- 1 Heterozygous SNPs: gDNA MAF < 0.15 (false positive rate=8/541=1.5%)
- 2 cDNA MAF<0.4;
- 3 Chi-square > 6.64 (p=0.01, df =1);
- 4 Three categories:
- Balanced;
- Imbalanced;
- Uncertain;
- 5 Three level ofs confidence
- Consistent: at least two SNPs with the consistent pattern.
- Probably: only one SNPs in a gene.
- Conflicting: two or more SNPs showing conflicting patterns.
Summary of Solexa runs
ID | Agilent Lib | Probe prep | Sample | Capturing reaction | Sample shipped | Solexa run |
1 | CES22k | ?? | NA10835 gDNA | ??, did by Billy | 11/8/2007 | 11/17/2007(good) |
2 | CES22k | ?? | NA20431 gDNA | ??, did by Billy | 11/8/2007 | 11/17/2007(good) |
3 | CES22k | ?? | GM20431 cDNA | ??, did by Billy | 11/8/2007 | 11/17/2007(good) |
4 | CES22k | ?? | GM20431 cDNA | ??, did by Billy | 11/8/2007 | 11/17/2007(good) |
5 | CES22k, #3,#4,#5 pooled | 11/9/2007 | NA20431 gDNA (347ng/ul) | 11/20/2007 | 11/26/2007 | 11/29/2007 (good) |
6 | CES22k, #3,#4,#5 pooled | 11/9/2007 | GM20431 cDNA (121ng/ul) | 11/20/2007 | 11/26/2007 | 11/29/2007 (good) |
7 | CES22k, #3,#4,#5 pooled | 11/9/2007 | GC1F cDNA | 11/20/2007 | 11/26/2007 | 11/29/2007 (good) |
8 | CES22k, #3,#4,#5 pooled | 11/9/2007 | GC1EP cDNA | 11/20/2007 | 11/26/2007 | 11/29/2007 (good) |
9 | CES22k | ?? | GC1F cDNA | ??, did by Billy | 11/8/2007 | 12/05/2007(good) |
10 | CES22k | ?? | GC1EP cDNA | ??, did by Billy | 11/8/2007 | 12/05/2007(good) |
11 | eSNP84k | 11/6/2007 | Hues6 gDNA | 11/11/2007 | 11/14/2007 | 12/05/2007(good) |
12 | eSNP84k | 11/6/2007 | Hues6 cDNA | 11/11/2007 | 11/14/2007 | 12/05/2007(good) |
13 | CES22k, #5, 10783810008 | 12/6/2007 127nM | NA20431 gDNA (347ng/ul) | 12/9/2007 | 12/17/2007 | 12/19/2007 (failed), 01/15/2008 (good) |
14 | CES22k, #5, 10783810008 | 12/6/2007 127nM | GM20431 cDNA (121ng/ul) | 12/9/2007 | 12/17/2007 | 12/19/2007 (failed), 01/15/2008 (good) |
15 | CES22k, #5, 10783810008 | 12/6/2007 127nM | GC1F cDNA (48ng/ul) | 12/9/2007 | 12/17/2007 | 12/19/2007 (failed) |
16 | CES22k, #5, 10783810008 | 12/6/2007 127nM | GC1EP cDNA (52ng/ul) | 12/9/2007 | 12/17/2007 | 12/19/2007 (failed) |
17 | CES22k, #5, 10783810008 | 1/12/2008 | NA20431 gDNA (347ng/ul) | 1/13/2008 | 1/17/2008 | 01/19/2008 (good) |
18 | CES22k, #5, 10783810008 | 1/12/2008 | GM20431 cDNA (121ng/ul) | 1/13/2008 | 1/17/2008 | 01/19/2008 (good) |
19 | CES22k, #5, 10783810008 | 1/12/2008 | GC1F cDNA (57ng/ul) | 1/13/2008 | 1/17/2008 | 01/19/2008 (good) |
20 | CES22k, #5, 10783810008 | 1/12/2008 | GC1EP cDNA (114ng/ul) | 1/13/2008 | 1/17/2008 | 01/19/2008 (good) |