??????????? ???? Affymetrix

1
??????? ?????????? (????????) ??????????? ?
?????????? ? ??????? ?????? ??? ??? ?????????
????? ????. ????????? ? ??????????? ???? ????????
???? ?????? ????????. ?? ???? ????????? ????? ?
??????? ???????????? ??????????? ??????? ???????
?? ????? ?????? ??????.
2
??????????? ???? Affymetrix
PM perfect match
MM mismatch
3
????? ????????? ??? ????? Affymetrix (?????
Affymetrix)

• ???????? ? ????? (gridding)
• ?????????? ???????? ????????????? ??????
• 3. ???????? ?? ?????????? ???
• 4. ???????? ?? ??????????????? ????????????
• 5. ?????????? ??????????? ???????? ??????????
  ???????????? ???????? ? ??????.
• 6. ??????????????? ???????? ????? ???????????
  ??????? ????? ????????????? ????????

4
???????? ??????????????? ???????1. MMgtPM
(60-85 ?????, ??? ??? ??????????? ???? ?? ???
?????? ?????)
??????? ?)
???????? Affymetrix ????????? mismatch ?) ? MM
?????? ?? ?????. ????????????? ???????? ?? ??? ?
?????? RMA. ?) ???, ???-???? ????? ????????????
MM, ?? ? ?????? ???????????? ????????????
???????? ?????? ?????????????????
??????????????????. GC-RMA
5
???????? ??????????????? ???????2. ?????? ?????
???????? ????????????? ?????? ????, ??????????
??????? ??????? ?? ????????.
?????? ??-?????. Eg ???????? ?????????? ???? g,
fi ???????????????? i-?? ???? PM-MM. PMgi
MMgi fi Eg ??? ???????????? ??????????,
??????????? ??? ????????????? (f12 fk2)/k 1
6
?????????? ???????? ?? ??????????? ??????????
??????????? ?? ?????????????. ?-? ??????.
Mglog(Ig(1)/Ig(2)) Ag(1/2)log(Ig(1)Ig(2))
M 0
A
7
???????? ??????????????? ???????3. ??????????
??????????? ?? ?????????????.
Mglog(Ig(1)/Ig(2)) Ag(1/2)log(Ig(1)Ig(2))
8
???????? ????????? 1
y abx
MINa,b((y1-(abx1))2(y2-(abx2))2(yk-(abxk))2
)
9
???????? ????????? 2

• ????? ?????? ??????? ??????? ? ???????? ?????????
  ????? ??????? ??????? ???????? ??????????
  ???????.
• ????????? ? ?????? ?????? ???????? ????????
  ???????????? ?????????? ? ? ?.

10
???????? ????????? 3

• ????? ? ???????? ?????? ????????? ???????
  ?????????????????? ?????????? ??? ? ? ?.
• ????? ????????? ??????, ????? ????? ????????????
  ???? ?????? ????? ????? ????? ??????? ???
• y Rx
• R ??????????? ?????????? ? ? ?. ??? ?????
  ?????? ?????? ????????? ? ????? ???????
• R(x1y1x2y2xnyn)/n

R0.0995, y 0.995x
11
????????-???????? ????????? (loess)
12
?? ?????? ????? ????????????
Mn M Mloess(A)
13
??????????? ????????????
14
??????????? ????????????
15
?? ??????? ??? ????????? ?????? ????????
???? ????????
16
????? ????? ? ?????????? ??????? ?????????? ?
?????? ????????

• Housekeeping ????
• ? ?????????, ?? ??? housekeeping ???? ?????
  ??????????? ??????? ??????????. ??????? b
  -?????, GAPDH,
• 2. ???? ????????????? ?????
• 3. ??????????? ????
• ???????? ???????????? bioB, bioC, bioD ? cre ????
  E. coli ? ?/? P1, ????????????????? ?RNA
  ??????????? ??????? ?????? ? ????? ???
  ???????????? ? ?????? ????????????? (1,5, 5, 25,
  100 pM ??? bioB, bioC, bioD ? cre, ?????.). BioB
  ?? ?????? ???????????????? (1100000).

17
????????? ?????????????????? ?????? ????????? ???
????? Affymetrix
1 ?????????? ????? ???????? ?????????????
?????? (Affymetrix MicroArray Suit) 2. ????????
?? ?????????? ??? (Affymetrix MAS5) 3. Loess
???????????? ?? ?????? ?????? (? PM ? MM
?????) 4. ?????????? ?????????? ???????
?????????? (?? ? ????, dChip) 6. ???????????
???????????? ???????? ??????????
18
???? ? ??? ????????????

• ? ??????????? ? ????? ???????????? ??????????? ?
  ???? ?????. ??? ???????????? ???????????? ?????
  ???? ????? ???????? (??????) ??????? ??? ?
  ??????????? ??? ? ????.
• ?) ??????? ??? ??? ???????
  ???????????? ???, ?????????? ??????.
• ?) ??????? ??? ??????????????. ???
  ???????, ??? ???, ??? ???????? ??????? ???? ?????
  ??????? ????????? ???????? ????? ???? ?? ????
  ?????, ??????? ??????? ?????????????.
• 2. ??? ??????????? ???????????? ????? ???????
  ????????????? ??????? ???? ? ????????? ???????
  ????????? ??? ? ????????? ?????????
  ?????????????, ???????????? ?? ???? ????? ?????.
• 3. ??? ????? ???????????? ?????????? ????????
  ??????????? ?????.

19
??? ????? ???????? ??? ??? Choe et al. Genome
Biology 2005, 6R16
 
1
1 14000 ????? ?? ????
 2551
1.2
87
2
1
141
1.5
1
85
2.5
1.2
1
1
3
180
1
90
2.0
88
1
1.5
2 14000 ????? ?? ????
1
186
4
1
1.7
90
1
180
1
183
1
20
??? ????? ???????? ???-????

• ?) Choe et al. Genome Biology 2005,
  6R16
• ????????? ?????? ??? ??? ????????, ????? ??????
  ???? ????????????????
• ????? ????? ?? ?????? ???? ?????? ?? ??????,
  ????????? ????? ?????, 10 ???????????
  ????????????? ?????, ? ????????? ???????? ??????
  60 ?????????????? ?????
• ????? ?? ?????? ????? ?? ?????, ????????? ?????
  ?????, 10 ??????????? ????????????? ?????, ?
  ????????? ???????? 85 ?????????????? ?????.

21
??? ????? ???????? ???-????

• ?) Choe et al. Genome Biology 2005,
  6R16
• ????????? ?????? ??? ??? ????????, ?????
  ???? ??????????????? ????????????????
• ?????, ???? ???????, ??? ???????????????
  ????????????????? ???????? ????????????? ?????
  ??? ?? 20 (?? 1309 ????? 380 ?? ????????? (29),
  ? ???????? ????????? 105(10 ?? ???? ?????????).
  ?? ????? ???? ?? ???? ?? ?????, ???????????
  ?????????? ?? 20 ?? ??? ??????, ? ???? ????????
  ???????????? ?? 50 ???? ???????.
• ??????, ???? ????????????? ???? ????, ??????????
  ?????????? ????? ??? ?? 100 (?? ????????? ????
  7 ?? ??? ???????????? ??? 10 ???????? ?????????
  )

22
???????? ?? ????????? ??????????? ?????????
??????????????

• ? ??????
• Multiple Lab Comparison of Microarray Platforms,
• Rafael A. Irizarry et al., 2004
• ??????????????? ?????????? ????????? ????? ? ???
  ?? ???????? ??????? ????????????? ?? ??????
  ??????????. ?????? ??????????? ????? ????? ?
  ??????????? ?????? ?????????.
• ???????, ??? ?????? ????????????, ???????? ?????,
  ??? ??? ??????? ????????????? ? ??????
  ?????????????????? ???????, ????????
  ?????????????? ??????????? ??????????
  ????????????, ?????????? ??????????? ?????????
  ?????????????.

23
??????????

• Exploration and analysis of DNA microarray and
  protein array data. D. Amaratunga, J. Cabrera,
  Wiley 2004.
• Statistical analysis of gene expression
  microarray data. Edited by T. Speed. Chapman and
  Hall, 2003.
• Statistics for microarrays. E. Wit, J. McClure,
  Wiley, 2004
• Analyzing microarray gene expressing data.
  G. McLachlan, Kim-Anh Do, C.
  Ambroise, Wiley, 2004
• Bioinformatics and computational biology
  solutions using R and Bioconductor. R. Gentleman,
  V. Carey, W. Huber, R. Irizzary, S. Dudoit,
  Springer, 2005.