Question: RUVnormalize- How to output a corrected expression matrix without negative values to use for DEG analysis(i.e. limma) ?
gravatar for massimo.acquaviva.78
4 days ago by
massimo.acquaviva.780 wrote:

Dear Supporters,

I'm using RUVnormalize package to correct a noisy dataset using negative controls. The input I'm using is a log2 expression matrix (Illumina V4 microarray) and I'm using naiveRandRUV function. Everything goes fine except that the output matrix from naiveRandRUV has very low values centered at 0 (with a lot of negative values). Am I doing something wrong or there is some option I don't know to output a normal uncentered log2 matrix (as for example does RUVseq) ?

Thank you in advance for your help

Massimo Acquaviva


San Raffaele Institute      Milan   Italy

ADD COMMENTlink modified 3 days ago by Dario Strbenac1.4k • written 4 days ago by massimo.acquaviva.780
gravatar for Dario Strbenac
3 days ago by
Dario Strbenac1.4k
Dario Strbenac1.4k wrote:

naiveRandRUV ​outputs the dataset with numbers compressed around 0. It's just a characteristic of the method. I like to avoid using RUV unless the PCA or MDS plot indicates that it's necessary.

ADD COMMENTlink written 3 days ago by Dario Strbenac1.4k

Thank you very much for your help

ADD REPLYlink written 11 minutes ago by massimo.acquaviva.780
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