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Alessio Venier
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40
@alessio-venier-1766
Last seen 10.3 years ago
Hi,
I'm using the limma package (2.7.5) to analyze data from spotted
microarray, I've used the read.maimage function
to load the raw data from files generated by bluefuse (this files also
contain intensities from blank spots).
Vesion 2.7.5 is working fine now when loading more than one file per
time (thanks to Gordon K Smyth and Mike Smith).
I would like to use the vsn normalization method (I've installed the
vsn R package).
I'm wondering if the intensity values from blank spots could create
problems with normalization process from
a mathematical point of view when applying vsn normalization method.
If it's the case I would like to "filter" the blank spots using R
instead of bluefuse features.
I've tried to assign NA values to all the blank spots intensities for
all channels/arrays but when I try to use
the vsn function I receive a message error becouse this function
doesn't allow NA values in in the data
to be analyzed. I don't understand how to use the subsample argument
in vsn to solve my problem.
It requires an integer value to define a subsample but I would require
a logic value
(something like: use only non NA values).
Any advice?
Kind Regards
Alessio