Hosuk:LabNotes/2014-2-9: Difference between revisions
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=====1 bit Error cases of Decode Binary String===== | =====Allowing 1 bit Error cases of Decode Binary String===== | ||
*EGFR_T790M_WT | *EGFR_T790M_WT | ||
**Normal : '01010010' | **Normal : '01010010' | ||
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====Result==== | ====Result==== | ||
{| {{table}} border = 1 | |||
{| {{table}} border = | |||
| align="center" style="background:#f0f0f0;"|'''Position''' | | align="center" style="background:#f0f0f0;"|'''Position''' | ||
| align="center" style="background:#f0f0f0;"|'''1''' | | align="center" style="background:#f0f0f0;"|'''1''' | ||
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| align="center" style="background:#f0f0f0;"|'''Std''' | | align="center" style="background:#f0f0f0;"|'''Std''' | ||
|- | |- | ||
| align="center" | EGFR_T790M_WT | | align="center" | EGFR_T790M_WT||align="center" | || align="center" | || align="center" | || align="center" | || align="center" | | ||
|- | |||
| align="center" | 01010010||align="center" | 4 || align="center" | 2 || align="center" | 6 || align="center" | 4 || align="center" | 2 | |||
|- | |||
| align="center" | 01010000||align="center" | 5 || align="center" | 14 || align="center" | 16 || align="center" | 11.67 || align="center" | 5.86 | |||
|- | |||
| align="center" | 01000010||align="center" | 3 || align="center" | 2 || align="center" | 1 || align="center" | 2 || align="center" | 1 | |||
|- | |||
| align="center" | 00010010||align="center" | 4 || align="center" | 12 || align="center" | 10 || align="center" | 8.67 || align="center" | 4.16 | |||
|- | |||
| align="center" | EGFR_T790M_MU||align="center" | || align="center" | || align="center" | || align="center" | || align="center" | | |||
|- | |||
| align="center" | 10100001||align="center" | 0 || align="center" | 0 || align="center" | 2 || align="center" | 0.67 || align="center" | 1.15 | |||
|- | |||
| align="center" | 10100000||align="center" | 1 || align="center" | 1 || align="center" | 2 || align="center" | 1.33 || align="center" | 0.58 | |||
|- | |||
| align="center" | 10000001||align="center" | 1 || align="center" | 1 || align="center" | 0 || align="center" | 0.67 || align="center" | 0.58 | |||
|- | |||
| align="center" | 00100001||align="center" | 0 || align="center" | 0 || align="center" | 0 || align="center" | 0 || align="center" | 0 | |||
|- | |||
| align="center" | EGFR_L858R_WT||align="center" | || align="center" | || align="center" | || align="center" | || align="center" | | |||
|- | |||
| align="center" | 10010100||align="center" | 3 || align="center" | 6 || align="center" | 8 || align="center" | 5.67 || align="center" | 2.52 | |||
|- | |||
| align="center" | 10010000||align="center" | 5 || align="center" | 11 || align="center" | 18 || align="center" | 11.33 || align="center" | 6.51 | |||
|- | |- | ||
| align="center" | | | align="center" | 10000100||align="center" | 4 || align="center" | 7 || align="center" | 5 || align="center" | 5.33 || align="center" | 1.53 | ||
|- | |- | ||
| align="center" | 00010100||align="center" | 2 || align="center" | 28 || align="center" | 22 || align="center" | 17.33 || align="center" | 13.61 | |||
|- | |||
| align="center" | | |||
|- | |||
| align="center" | EGFR_L858R_MU||align="center" | || align="center" | || align="center" | || align="center" | || align="center" | | |||
|- | |||
| align="center" | 01001001||align="center" | 0 || align="center" | 0 || align="center" | 0 || align="center" | 0 || align="center" | 0 | |||
|- | |||
| align="center" | 01001000||align="center" | 0 || align="center" | 0 || align="center" | 1 || align="center" | 0.33 || align="center" | 0.58 | |||
|- | |||
| align="center" | 01000001||align="center" | 17 || align="center" | 12 || align="center" | 6 || align="center" | 11.67 || align="center" | 5.51 | |||
|- | |||
| align="center" | 00001001||align="center" | 1 || align="center" | 0 || align="center" | 1 || align="center" | 0.67 || align="center" | 0.58 | |||
|} | |} | ||
*Matlab code : Rolony_Decoding_v6.m |
Revision as of 06:22, 10 February 2014
NCIH1975 : Mutation Detection : 2nd Try, Data Analysis
- Data from 2/3
- Took pictures at 3 Positions on the sample in MatTek dish
Procedure
- Maximum projection image with all images of 8 steps
- Run PISA to make BW images
- Use the BW image as mask image file and do masking an each image (=image file .* mask image)
- Run PISA with masked image, and obtain a number of rolonies, centroid coordinate information of each rolony
- Decode the rolony to extract decoding information along steps
Major Parameters
Decode Binary table of each target
EGFR_T790M_WT | EGFR_T790M_MU | EGFR_L858R_WT | EGFR_L858R_MU | |
Step1 (1FAM) | 0 | 1 | 0 | 1 |
Step2 (1Cy3) | 1 | 0 | 0 | 0 |
Step3 (2FAM) | 0 | 0 | 1 | 0 |
Step4 (2Cy3) | 0 | 0 | 0 | 1 |
Step5 (3FAM) | 1 | 0 | 1 | 0 |
Step6 (3Cy3) | 0 | 1 | 0 | 0 |
Step7 (4FAM) | 1 | 0 | 0 | 1 |
Step8 (4Cy3) | 0 | 1 | 1 | 0 |
Decode Binary String of each target
- EGFR_T790M_WT = '01010010'
- EGFR_T790M_MU = '10100001'
- EGFR_L858R_WT = '10010100'
- EGFR_L858R_MU = '01001001'
Allowing 1 bit Error cases of Decode Binary String
- EGFR_T790M_WT
- Normal : '01010010'
- Error 1 : '01010000'
- Error 2 : '01000010'
- Error 3 : '00010010'
- EGFR_T790M_MU
- Normal : '10100001'
- Error 1 : '10100000'
- Error 2 : '10000001'
- Error 3 : '00100001'
- EGFR_L858R_WT
- Normal : '10010100'
- Error 1 : '10010000'
- Error 2 : '10000100'
- Error 3 : '00010100'
- EGFR_L858R_MU
- Normal : '01001001'
- Error 1 : '01001000'
- Error 2 : '01000001'
- Error 3 : '00001001'
Result
Position | 1 | 2 | 3 | Avg | Std |
EGFR_T790M_WT | |||||
01010010 | 4 | 2 | 6 | 4 | 2 |
01010000 | 5 | 14 | 16 | 11.67 | 5.86 |
01000010 | 3 | 2 | 1 | 2 | 1 |
00010010 | 4 | 12 | 10 | 8.67 | 4.16 |
EGFR_T790M_MU | |||||
10100001 | 0 | 0 | 2 | 0.67 | 1.15 |
10100000 | 1 | 1 | 2 | 1.33 | 0.58 |
10000001 | 1 | 1 | 0 | 0.67 | 0.58 |
00100001 | 0 | 0 | 0 | 0 | 0 |
EGFR_L858R_WT | |||||
10010100 | 3 | 6 | 8 | 5.67 | 2.52 |
10010000 | 5 | 11 | 18 | 11.33 | 6.51 |
10000100 | 4 | 7 | 5 | 5.33 | 1.53 |
00010100 | 2 | 28 | 22 | 17.33 | 13.61 |
EGFR_L858R_MU | |||||
01001001 | 0 | 0 | 0 | 0 | 0 |
01001000 | 0 | 0 | 1 | 0.33 | 0.58 |
01000001 | 17 | 12 | 6 | 11.67 | 5.51 |
00001001 | 1 | 0 | 1 | 0.67 | 0.58 |
- Matlab code : Rolony_Decoding_v6.m