Hi Maria,

please have a look at the help page of the function "preprocess". The arguments "ChIPChannel" and "inputChannel" allow you to specify which components of the RGList correspond to the ChIP data (which you probably mean by "output") and the control/input data. By default, Cy5 is the ChIP and Cy3 the input, but using those arguments you can override the default, so there is no need to switch around components of the list.


Please also have a look at the vignette of the package, which can also be found online here:
http://bioconductor.org/packages/release/bioc/vignettes/Ringo/inst/doc/Ringo.pdf
which shows how to work with different kinds of raw microarray data.


Please let me know if you have further questions.

Best regards,
Joern




Maria Arnedo <MariaArnedo@> schrieb am 13:00 Montag, 28.Juli 2014:
 


Hello everybody!

I am making the analysis of my arrays with the Ringo package and I have a couple of questions about the normalization. 

I have label my input with Cy5 and the output with Cy3, but I don't know if the Ringo package assumes that Cy5 is the input and Cy3 the output or vice-versa, when I make the vsn normalization of my data. Which one the Ringo package assume as a input? If it is the opposite way that I have labelled them, how can I make the analysis?

Thank you in advance

Best Regards,

Maria

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