RUVnormalize- How to output a corrected expression matrix without negative values to use for DEG analysis(i.e. limma) ?
1
0
Entering edit mode
@massimoacquaviva78-14767
Last seen 6.8 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) ?

Thank you in advance for your help

Massimo Acquaviva

Bioinformatician

San Raffaele Institute      Milan   Italy

RUVnormalize limma corrected expression matrix microarray • 1.2k views
ADD COMMENT
0
Entering edit mode
Dario Strbenac ★ 1.5k
@dario-strbenac-5916
Last seen 4 days 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.

ADD COMMENT
0
Entering edit mode

Thank you very much for your help

ADD REPLY

Login before adding your answer.

Traffic: 653 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6