[BioC] tilingArray- normalizeByReference

Joern Toedling toedling at ebi.ac.uk
Tue Oct 28 11:07:41 CET 2008

Hello Anjan,

well, the error message indicates that your vector pm_vector is not
usable by the function. Is it really an integer vector. What is the
output of
Probably, it would be better to read in the file by something like
pm_vector <- read.delim("PerfectMatchIndex", skip=<put number of header
lines here!>)$V1
Again, check the result using
If you want to use other functionalities of package tilingArray, you
should consider creating a 'probeAnno' environment, which holds the
mapping between probes and genomic match positions, for your array.
Please see the script "makeProbeAnno.R" in the package's "scripts"
directory for details. Once you have such a probeAnno object, the
function "PMindex" can be used to obtain a numeric vector that you can
use as "pm" in the normalization function.
Please see the vignette "assessNorm" of package tilingArray for more

Best regards,

Anjan Purkayastha wrote:
> 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 target.
> 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?
> tia
> anjan

Joern Toedling
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom
Phone  +44(0)1223 492566
Email  toedling at ebi.ac.uk

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