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 ï¾µm 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 [[alternative HTML version deleted]]

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