Question: limma voom problem
0
gravatar for iskysinger
5 days ago by
iskysinger0
iskysinger0 wrote:

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

voom rna-seq limma next-gen R • 101 views
ADD COMMENTlink modified 4 days ago by Kevin Blighe53k • written 5 days ago by iskysinger0

Which of these columns indicate the experimental groups? You do not plan to use all these parameters for your model, right?

ADD REPLYlink modified 5 days ago • written 5 days ago by ATpoint28k

added limma and voom tags

ADD REPLYlink written 4 days ago by Kevin Blighe53k
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