[BioC] Basic Question

Marcus Albrecht albrec_m at molgen.mpg.de
Mon Aug 30 13:18:45 CEST 2004


Hi,
I'm new into Affymetrix data evaluation and using Bioconductor, so sorry 
in advance for asking trivial questions. I was doing some testing with 
expresso and noticed something that I don't understand:

my expresso command:      eset <- expresso(Data, bg.correct=FALSE, 
normalize=FALSE, pmcorrect.method="pmonly", summary.method="avgdiff")
This schould do no background correction, no normalization, summarize 
only perfect matches and calculate the average of them. Here's a small 
snippet from one of my cel files and the coressponding cdf file:

cel file:

[INTENSITY]
NumberCells=285156
CellHeader=X    Y    MEAN    STDV    NPIXELS
237     61    183.3    31.3     36
237     62    292.5    52.0     36
238     61    196.0    20.0     36
238     62    243.0    74.2     36
239     61    88.5    15.7     36
239     62    94.3    12.2     36
240     61    93.3    13.9     36
240     62    82.3    11.8     36
241     61    128.3    18.7     36
241     62    134.0    18.4     36
242     61    116.3    16.7     36
242     62    101.5    20.6     36
243     61    113.8    22.0     36
243     62    127.5    16.8     36
244     61    296.5    39.3     36
244     62    146.3    19.5     36
245     61    116.5    19.8     36
245     62    112.3    18.7     36
246     61    81.3    11.0     36
246     62    82.0    12.2     36
247     61    159.3    23.1     36
247     62    92.8    13.6     36
248     61    122.8    19.3     36
248     62    134.8    21.4     36
249     61    316.3    37.1     36
249     62    1122.5    96.6     36
250     61    89.3    14.6     36
250     62    98.0    15.9     36
251     61    244.0    32.2     36
251     62    175.5    23.1     36
252     61    8075.8    1063.4     36
252     62    705.5    73.2     36

cdf file:

[Unit1075_Block1]
Name=A01157cds_s_at
BlockNumber=1
NumAtoms=16
NumCells=32
StartPosition=0
StopPosition=15
CellHeader=X    Y    PROBE    FEAT    QUAL    EXPOS    POS    CBASE    
PBASE    TBASE    ATOM    INDEX    CODONIND    CODON    REGIONTYPE    REGION
Cell1=237    61    N    control    A01157cds_s_at    0    13    T    
A    T    0    32811    -1    -1    99   
Cell2=237    62    N    control    A01157cds_s_at    0    13    T    
T    T    0    33345    -1    -1    99   
Cell3=238    62    N    control    A01157cds_s_at    1    13    A    
A    A    1    33346    -1    -1    99   
Cell4=238    61    N    control    A01157cds_s_at    1    13    A    
T    A    1    32812    -1    -1    99   
Cell5=239    61    N    control    A01157cds_s_at    2    13    T    
A    T    2    32813    -1    -1    99   
Cell6=239    62    N    control    A01157cds_s_at    2    13    T    
T    T    2    33347    -1    -1    99   
Cell7=240    62    N    control    A01157cds_s_at    3    13    A    
A    A    3    33348    -1    -1    99   
Cell8=240    61    N    control    A01157cds_s_at    3    13    A    
T    A    3    32814    -1    -1    99   
Cell9=241    61    N    control    A01157cds_s_at    4    13    G    
C    G    4    32815    -1    -1    99   
Cell10=241    62    N    control    A01157cds_s_at    4    13    G    
G    G    4    33349    -1    -1    99   
Cell11=242    62    N    control    A01157cds_s_at    5    13    A    
A    A    5    33350    -1    -1    99   
Cell12=242    61    N    control    A01157cds_s_at    5    13    A    
T    A    5    32816    -1    -1    99   
Cell13=243    62    N    control    A01157cds_s_at    6    13    C    
C    C    6    33351    -1    -1    99   
Cell14=243    61    N    control    A01157cds_s_at    6    13    C    
G    C    6    32817    -1    -1    99   
Cell15=244    62    N    control    A01157cds_s_at    7    13    A    
A    A    7    33352    -1    -1    99   
Cell16=244    61    N    control    A01157cds_s_at    7    13    A    
T    A    7    32818    -1    -1    99   
Cell17=245    61    N    control    A01157cds_s_at    8    13    G    
C    G    8    32819    -1    -1    99   
Cell18=245    62    N    control    A01157cds_s_at    8    13    G    
G    G    8    33353    -1    -1    99   
Cell19=246    61    N    control    A01157cds_s_at    9    13    T    
A    T    9    32820    -1    -1    99   
Cell20=246    62    N    control    A01157cds_s_at    9    13    T    
T    T    9    33354    -1    -1    99   
Cell21=247    61    N    control    A01157cds_s_at    10    13    G    
C    G    10    32821    -1    -1    99   
Cell22=247    62    N    control    A01157cds_s_at    10    13    G    
G    G    10    33355    -1    -1    99   
Cell23=248    61    N    control    A01157cds_s_at    11    13    G    
C    G    11    32822    -1    -1    99   
Cell24=248    62    N    control    A01157cds_s_at    11    13    G    
G    G    11    33356    -1    -1    99   
Cell25=249    62    N    control    A01157cds_s_at    12    13    C    
C    C    12    33357    -1    -1    99   
Cell26=249    61    N    control    A01157cds_s_at    12    13    C    
G    C    12    32823    -1    -1    99   
Cell27=250    62    N    control    A01157cds_s_at    13    13    C    
C    C    13    33358    -1    -1    99   
Cell28=250    61    N    control    A01157cds_s_at    13    13    C    
G    C    13    32824    -1    -1    99   
Cell29=251    61    N    control    A01157cds_s_at    14    13    G    
C    G    14    32825    -1    -1    99   
Cell30=251    62    N    control    A01157cds_s_at    14    13    G    
G    G    14    33359    -1    -1    99   
Cell31=252    62    N    control    A01157cds_s_at    15    13    C    
C    C    15    33360    -1    -1    99   
Cell32=252    61    N    control    A01157cds_s_at    15    13    C    
G    C    15    32826    -1    -1    99   

If I am doing the calculation by hand the result for A01157cds_s_at is 
234.05, but expresso gives me 125.55. Am I doing something wrong or 
what's the reason behind this? Thanks in advance ...

Cheers
Marcus

-- 
===================================================================
Marcus Albrecht		Max-Planck-Institute for Molecular Genetics
Department Lehrach	Bioinformatics Group
Harnackstrasse 23	e-mail:	albrec_m at molgen.mpg.de
14195 Berlin		Telephone: ++49 - (0)30 - 8413 1682



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