[BioC] tilingArray- normalizeByReference

Anjan Purkayastha purkayas at wi.mit.edu
Mon Oct 27 22:15:03 CET 2008

hi all,
a rookie tilingArray question.
i'm having trouble creating the perfect match index vector.
for my probe set (n= 6490), each probe is a unique, perfect match to its 
i have created a probe index file that contains the integers: 1, 
2....6490 (one index per line).
i scanned this file as:  pm_vector <- scan("PerfectMatchIndex", 0)

i used the pm_vector in a following command:
vac_normalized_exp_data <- normalizeByReference(vac_exp_set, 
vac_hyb_set, pm= pm_vector, background= bg_vector, cutoffQuantile= 0)

this gives me an error:
 'pm' must be an integer vector with values between 1 and 6490.

any idea what the problem could be?

anjan purkayastha, phd
bioinformatics analyst
whitehead institute for biomedical research
nine cambridge center
cambridge, ma 02142

purkayas [at] wi [dot] mit [dot] edu  

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