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Question: RUVnormalize- How to output a corrected expression matrix without negative values to use for DEG analysis(i.e. limma) ?
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gravatar for massimo.acquaviva.78
11 months 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

Bioinformatician

San Raffaele Institute      Milan   Italy

ADD COMMENTlink modified 11 months ago by Dario Strbenac1.4k • written 11 months ago by massimo.acquaviva.780
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gravatar for Dario Strbenac
11 months ago by
Dario Strbenac1.4k
Australia
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 11 months ago by Dario Strbenac1.4k

Thank you very much for your help

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