Design matrix in limma

Design matrix in limma

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I have quantile normalized counts, with negative values: The data sets is:

GeneID 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016

1/2-SBSRNA4 1.84545405543259 0.6665398175808 1.59873554207786 1.89298926465623 1.26568208427265 1.88410700890907 1.74378606410793 1.48987360722618
A1BG 1.6165355686345 2.68681326811308 1.50663367983524 2.25377918290859 2.67375515222443 2.37256130394363 2.98553798816952 2.7872063927308 2.46972065233526
A1BG-AS1 0.0318256718292522 1.06223446343374 0.365739932809055 0.160454525989031 -0.189562119063132 0.451464743899586 1.00348737045778 0.521080706070493
A2LD1 2.42805396344275 3.29182280645954 3.42740052556388 3.54573585005455 2.6718279086933 2.84892844820465 3.23788385068264 2.5512302536277 3.00143277095887
A2M 8.69286445805741 9.01321493190288 9.06178519781115 9.37509171855292 9.15365897313587 10.225835039655 9.58498357891138 9.26308027293732 10.10798379

This data set has zeros. I have no idea about the comparisons between samples. I am new in limma

Kindly help me


Limma


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