Ylaine/2009-8-26: Difference between revisions

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>Ylaine
Line 20: Line 20:


==False Negatives==
==False Negatives==
 
cat gold.covereda*>gold.covered
../Scripts/matchGold.pl gold.covered>gold.match
** 9553 total: 7869 match, 1182 miss, 512 mismatch
../Scripts/threshold.pl gold.match 2 > gold.match2
{| {{table}}
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''Correct SNP'''
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''Incorrect'''
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''Missed'''
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''Total'''
|-
| 1x||7859||82.27%||512||5.36%||1182||12.37%||9553
|-
| 2x||7715||85.97%||348||3.88%||911||10.15%||8974
|-
| 8x||6732||94.05%||57||0.80%||369||5.16%||7158
|-
| 20x||4997||96.37%||10||0.19%||178||3.43%||5185
|-
|
|}
[[Image:Aug17_fn.bmp]]


==Poster==
==Poster==
* Determine whom to acknowledge for experimental results
* Determine whom to acknowledge for experimental results

Revision as of 22:33, 26 August 2009

Clustering

  • Re-ran clustering with similar results. Only difference is 1 false SNP that was accepted in the first round instead of the second round.

File:Aug17 nodbSNP.jpg File:Aug17 cluster1.jpg File:Aug17 cluster2.jpg

  • Commands:
[error, groups] = snpCluster(match,miss);
    • 328 accepted, 3102 rejected, total error rate of 8.45% (46.46% MD, 1.42% FP)
    • 287 true and 41 false
groups_match = groups(1:536);
rejects_match = match(find(groups_match==2),:);
groups_miss = groups(537:3430);
rejects_miss = miss(find(groups_miss==2),:);

[error, groups2] = snpCluster(rejects_match, rejects_miss);
    • 214 accepted, 2888 rejected, total error rate of 6.61% (48.19% MD, 2.98% FP)
    • 129 true and 85 false
  • Validate method on another test set

False Negatives

cat gold.covereda*>gold.covered
../Scripts/matchGold.pl gold.covered>gold.match
    • 9553 total: 7869 match, 1182 miss, 512 mismatch
../Scripts/threshold.pl gold.match 2 > gold.match2
' Correct SNP ' Incorrect ' Missed ' Total
1x 7859 82.27% 512 5.36% 1182 12.37% 9553
2x 7715 85.97% 348 3.88% 911 10.15% 8974
8x 6732 94.05% 57 0.80% 369 5.16% 7158
20x 4997 96.37% 10 0.19% 178 3.43% 5185

File:Aug17 fn.bmp

Poster

  • Determine whom to acknowledge for experimental results