Hi everybody,

I have a question about the behavior of the expresso command when
extracting the raw data from an affyBatch.

I wanted to evaluate the raw intensities values of a specific gene from my
data set and tried to extract it like that:
rawdata <- expresso(totalExpressionData, bg.correct=FALSE,
                       normalize=FALSE,
                       pmcorrect.method="pmonly", summary.method="avgdiff",
                       verbose=TRUE)

I've got the result I wanted:
             wt1    wt2    wt3    treat1    treat2    treat3
gene_at    125.5    101    123.5    52.5    63.5    58

The problem was that i expected them to be the other way around.
So I decided to look into the specific probe values of the probes for this
probe-set.
This are the values I've got from the PM and MM respectively:
    wt1    wt2    wt3    treat1    treat2    treat3
probe1    403    379    220    420    530    316
probe2    117    84    104    52    57    54
probe3    49    49    73    38    58    52
probe4    87    67    110    55    43    49
probe5    66    61    51    46    72    62
probe6    118    100    104    69    87    74
probe7    180    142    170    45    46    45
probe8    133    102    137    95    132    81
probe9    80    71    65    52    54    46
probe10    63    45    56    53    53    54
probe11    293    321    260    444    618    408
probe12    171    167    169    49    75    72
probe13    198    197    307    40    67    50
probe14    247    265    348    53    60    62

probe1    533    519    294    507    739    404
probe2    1789    1271    1468    1430    1666    1552
probe3    56    66    59    51    45    48
probe4    49    52    64    47    45    47
probe5    54    47    33    49    65    55
probe6    84    72    90    53    92    71
probe7    73    72    65    40    53    54
probe8    83    108    115    81    111    94
probe9    49    56    43    52    41    53
probe10    56    46    62    68    77    57
probe11    54    83    55    47    64    46
probe12    106    98    76    52    66    53
probe13    43    48    37    36    52    39
probe14    94    92    99    43    43    49

When I calculate the average of these two tables for each array I don't get
the same values as presented in the top table.
I would like to understand how from the values on the last two tables I
come to a summarized value I get. Even if I ignore the MM values
completely, which I think it does, I still don't see how it comes to these
values. The two probes (Nr. 1 and 11 of the PM values) are strongly differ
from the rest of the probes for this probe-set. Are they being ignored in
the summarization?

Thanks in advance

Assa

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