Dear Members,

I've inherited a set of file regarding a microarray analysis experiment.
this is the header of one of my csv file.

BEGIN HEADER
PerkinElmer Inc.
ScanArrayCSVFileFormat    2
ScanArray Express    2
Number_of_Columns    26
END HEADER

BEGIN GENERAL INFO
DateTime    01/06/05 06:25 PM
GalFile    F:\Microarray Facility only\Facility documents\GAL\Human 19K
GAL.gal
Scanner    Model:  Serial No.:
User Name    JMa
Computer Name
Protocol    human19k
Quantitation Method    Adaptive Circle
Quality Confidence Calculation    Footprint
User comments
Image Origin    0
Temperature    0
Laser Powers    0
Laser On Time    0
PMT Voltages    0
END GENERAL INFO

BEGIN QUANTITATION PARAMETERS
Min Percentile    50
Max Percentile    200
END QUANTITATION PARAMETERS

BEGIN QUALITY MEASUREMENTS
Max Footprint    100
END QUALITY MEASUREMENTS

BEGIN ARRAY PATTERN INFO
Units    ﾵm
Array Rows    12
Array Columns    4
Spot Rows    20
Spot Columns    20
Array Row Spacing    4500
Array Column Spacing    4500
Spot Row Spacing    200
Spot Column Spacing    200
Spot Diameter    100
Interstitial    0
Spots Per Array    400
Total Spots    19200
END ARRAY PATTERN INFO

BEGIN IMAGE INFO
ImageID    Channel
-1    CH1
END IMAGE INFO

BEGIN NORMALIZATION INFO
Normalization Method    LOWESS
END NORMALIZATION INFO
...

as u can see they are single color arrays..
usually i work with affymetrix data, and this is the first time i treat
ScanArray Express.
looking for help on the mailing list archive, i found and test this code

RG <- read.maimages(files,source="scanarrayexpress",columns=list(G="Ch1\
Median", Gb="Ch1\ B\ Median",R="Ch1\ Median", Rb="Ch1\ B\ Median"), sep=",")

## read 4 .csv files in my wd that i will compare for differential
expression(is it correct??)

Read *******.csv
Read *******.csv
Read *******.csv
Read *******.csv
Warning messages:
1: In grep(a, txt) : input string 1 is invalid in this locale
2: In grep(a, txt) : input string 1 is invalid in this locale
3: In grep(a, txt) : input string 1 is invalid in this locale
4: In grep(a, txt) : input string 1 is invalid in this locale
5: In grep(a, txt) : input string 1 is invalid in this locale
6: In grep(a, txt) : input string 1 is invalid in this locale
7: In grep(a, txt) : input string 1 is invalid in this locale
8: In grep(a, txt) : input string 1 is invalid in this locale

## only warning, but..

RG$R <- NULL

## to remove the ch2

vsnMatrix(RG$G)
vsn: 19201 x 4 matrix (1 stratum).   0% done.Error: isSmall(rsv@mu - hmean)
is not TRUE

## Error!!

and if i try to normalize with normalizeWithinArrays cmd

normalizeWithinArrays(RG,method="none")
An object of class "MAList"
$targets
                                           FileName
****011205 ****011205.csv
****011305 ****011305.csv
****011305 ****011305.csv
****011405 ****011405.csv

$genes
  Array Row Array Column Spot Row Spot Column
1         1            1        1           1
2         1            1        1           2
3         1            1        1           3
4         1            1        1           4
5         1            1        1           5
19196 more rows ...

$source
[1] "scanarrayexpress"

$M
    ****011205     ****011305     ****011305
[1,]                      NA                      NA                      NA
[2,]                      NA                      NA                      NA
[3,]                      NA                      NA                      NA
[4,]                      NA                      NA                      NA
[5,]                      NA                      NA                      NA
     ****011405
[1,]                      NA
[2,]                      NA
[3,]                      NA
[4,]                      NA
[5,]                      NA
19196 more rows ...

$A
     ****011205 ****011305 ****011305
[1,]                      NA                      NA                      NA
[2,]                      NA                      NA                      NA
[3,]                      NA                      NA                      NA
[4,]                      NA                      NA                      NA
[5,]                      NA                      NA                      NA
     ****011405
[1,]                      NA
[2,]                      NA
[3,]                      NA
[4,]                      NA
[5,]                      NA
19196 more rows ...


hoping somebody could point me in the right direction..
thanks in advance..

lau

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