Dear,

I would like to normalize my microarray data based on an internal control that I inserted into my library.

There is some package in the Bioconductor for this purpose ?

I think that RMA package takes into account all the genes for normalization.

Are there any packages that take into account this specific internal control?

Thanks in advance for any help.

Leandro de Mattos

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There is no RMA package. Perhaps you mean the affy, oligo, or xps package (all of which have functions that perform RMA)? Also, what does 'I inserted into my library' mean, exactly? The term 'library' is usually used in reference to RNA-Seq, not microarray.

If you only have a single internal control, then you could hypothetically just run rma without normalizing, and then center the resulting data on the internal control. Both affy and oligo will allow you to do that, and I presume xps will as well. See the help page for rma in whatever package you are planning to use.

There are no (to my knowledge) functions that are specifically intended for this use-case, as it's a pretty uncommon thing to do.