RUVnormalize- How to output a corrected expression matrix without negative values to use for DEG analysis(i.e. limma) ?
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@massimoacquaviva78-14767
Last seen 4.6 years ago

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) ?

Massimo Acquaviva

Bioinformatician

San Raffaele Institute      Milan   Italy

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Dario Strbenac ★ 1.5k
@dario-strbenac-5916
Last seen 9 weeks ago
Australia

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.

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Thank you very much for your help