Hi, I was trying to use R limma package for the RNAseq DE analysis. I created a design (or model) matrix using model.matrix, and the design matrix is like this:
> design
f1LPL_CD3_minus f1LPL_CD3_plus RIN. Ribosomal.content Yield..ug. Exon.mapping.rate f3colon f3ileum
97 1 0 1.4537394 -0.25587959 0.1703515 1.52249759 1 0
98 1 0 -0.5372515 0.55320491 -0.7125984 -0.07822664 1 0
91 0 1 1.1693121 -0.16896496 -0.4363936 0.13894200 0 0
99 1 0 -1.3905334 -0.01870335 -0.5903438 0.60849125 1 0
92 0 1 0.6004576 -0.50248289 2.1535927 0.25607977 0 1
93 0 1 -0.2528242 -0.43028018 -0.6790916 -0.24759116 1 0
94 0 1 -1.1061061 -0.87528023 1.0940529 0.63935740 1 0
95 1 0 0.6004576 2.42297639 -0.2462197 -2.01941516 0 1
96 1 0 -0.5372515 -0.72459011 -0.7533499 -0.82013504 1 0
However, when I estimate the mean-variance relationship and use this to compute appropriate observational-level weights using voom, I get the following message:
Warning messages:
1: Partial NA coefficients for 14769 probe(s)
2: In voom(gExpr, design) :
The experimental design has no replication. Setting weights to 1.
Does anyone knows why there experimental design has no replication. Any help will be appreciated. Thanks a lot.
Andy
Which of these columns indicate the experimental groups? You do not plan to use all these parameters for your model, right?
Hi , Thanks for the reply. The f1LPL_CD3_minus and f1LPL_CD3_plus indicate the experimental groups and used for the comparison. The rest parameters are used as co-variants for the model.
added
limma
andvoom
tags