Hi all

I have 48 Affymetrix mogene data and my batch text file is as follows:

Name
        Batch

Affy1.CEL
        1

Affy2.CEL
        1

Affy3.CEL
        1

AffyA1.CEL
        2

AffyA2.CEL
        2








>library(SCAN.UPC)
> Sdata <- SCAN("*.CEL", convThreshold = 0.01, batchFilePath = "batchtargets1.txt", verbose = TRUE)

After completing the iterations, I get this message.

No batch covariates have been specified.
Getting ready to perform batch adjustment.
Found 2 batches
Found 0  categorical covariate(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding parametric adjustments
Error in while (change > conv) { : missing value where TRUE/FALSE needed

I eyeballed my Sdata that I did previously (using the following) but did not spot any NaN or missing values in the normalised values.

> Sdata <- SCAN("*.CEL", convThreshold = 0.01, verbose = TRUE)

I am not sure what went wrong. Can someone enlighten me?

Cheers

Joel Z Ma, PhD

Dept. of Microbiology and Immunology
The Peter Doherty Institute for Infection and Immunity
University of Melbourne
792 Elizabeth Street
Parkville
Victoria, 3000

Ph: +61 3 83440775
E-mail: jzma@unimelb.edu.au<mailto:jzma@unimelb.edu.au>




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