[BioC] limma warning: Coefficients not estimable
Karl Brand
k.brand at erasmusmc.nl
Wed Feb 10 17:08:34 CET 2010
Dear BioC,
Using limma, when fitting the model:
model.matrix(~Tissue * Pperiod + Time + Animal)
I get this warning:
> fit <- lmFit(rma.pp, design)
Coefficients not estimable: Animal32 Animal33 Animal34 Animal35 Animal36
Animal37 Animal38 Animal39 Animal40 Animal41 Animal42 Animal43 Animal44
Animal45 Animal46 Animal47 Animal48
Warning message:
Partial NA coefficients for 45101 probe(s)
In addition, the reuslting number or DE genes for my contrasts of
interest (which are different than the 'not estimable' ones listed in
teh warning above) are mcuh lower than expected; & furthermore, the
contrast-coefficents (log2FCs) and simply wrong.
When fitting a similar model, merely lacking the 'pairing' factor
("Animal"):
model.matrix(~Tissue * Pperiod + Time)
I don't get this error. My question:
Is it me? Or am i attempting the impossible, ie., by including a factor
for pairing (Animal) trying to fit more factors than my measurements can
support and this is limma's way of telling me? Raw script and targets
file below.
I really hope an experienced limma user can enlighten me on this, or
point me to a resource suitable for a biologists level of understanding.
Thanks in advance,
Karl
> targets <- read.delim("RNA_Targets.txt")
> Tissue <- factor(targets$Tissue, levels = c("R", "C"))
> Pperiod <- factor(targets$Pperiod, levels = c("E", "L", "S"))
> Time <- factor(targets$Time, levels = c("1", "2", "3", "4",
+ "5", "6", "7", "8",
+ .... [TRUNCATED]
> Animal <- factor(targets$Animal, levels = c("1", "2", "3", "4",
+ "5", "6", "7", "8",
+ .... [TRUNCATED]
> design <- model.matrix(~Tissue * Pperiod + Time + Animal)
> colnames(design)
[1] "(Intercept)" "TissueC" "PperiodL"
"PperiodS" "Time2" "Time3" "Time4"
"Time5" "Time6" "Time7"
[11] "Time8" "Time9" "Time10" "Time11"
"Time12" "Time13" "Time14"
"Time15" "Time16" "Animal2"
[21] "Animal3" "Animal4" "Animal5" "Animal6"
"Animal7" "Animal8" "Animal9"
"Animal10" "Animal11" "Animal12"
[31] "Animal13" "Animal14" "Animal15" "Animal16"
"Animal17" "Animal18" "Animal19"
"Animal20" "Animal21" "Animal22"
[41] "Animal23" "Animal24" "Animal25" "Animal26"
"Animal27" "Animal28" "Animal29"
"Animal30" "Animal31" "Animal32"
[51] "Animal33" "Animal34" "Animal35" "Animal36"
"Animal37" "Animal38" "Animal39"
"Animal40" "Animal41" "Animal42"
[61] "Animal43" "Animal44" "Animal45" "Animal46"
"Animal47" "Animal48" "TissueC:PperiodL"
"TissueC:PperiodS"
> source(.trPaths[5], echo=TRUE, max.deparse.length=150)
> fit <- lmFit(rma.pp, design)
Coefficients not estimable: Animal32 Animal33 Animal34 Animal35 Animal36
Animal37 Animal38 Animal39 Animal40 Animal41 Animal42 Animal43 Animal44
Animal45 Animal46 Animal47 Animal48
Warning message:
Partial NA coefficients for 45101 probe(s)
>
FileName Tissue Pperiod Time Animal
01-PPL3-sample02.CEL R S 1 1
02-PPL3-sample03.CEL C S 1 1
03-PPL5-sample02.CEL R S 2 2
04-PPL5-sample03.CEL C S 2 2
05-PPL3-sample04.CEL R S 3 3
06-PPL3-sample05.CEL C S 3 3
07-PPL5-sample04.CEL R S 4 4
08-PPL5-sample05.CEL C S 4 4
09-PPL3-sample06.CEL R S 5 5
10-PPL3-sample07.CEL C S 5 5
11-PPL5-sample06.CEL R S 6 6
12-PPL5-sample07.CEL C S 6 6
13-PPL3-sample08.CEL R S 7 7
14-PPL3-sample09.CEL C S 7 7
15-PPL5-sample08.CEL R S 8 8
16-PPL5-sample09.CEL C S 8 8
17-PPL3-sample10.CEL R S 9 9
18-PPL3-sample11.CEL C S 9 9
19-PPL5-sample10.CEL R S 10 10
20-PPL5-sample11.CEL C S 10 10
21-PPL3-sample12.CEL R S 11 11
22-PPL3-sample13.CEL C S 11 11
23-PPL5-sample12.CEL R S 12 12
24-PPL5-sample13.CEL C S 12 12
25-PPL3-sample14.CEL R S 13 13
26-PPL3-sample15.CEL C S 13 13
27-PPL5-sample14.CEL R S 14 14
28-PPL5-sample15.CEL C S 14 14
29-PPL3-sample16.CEL R S 15 15
30-PPL3-sample17.CEL C S 15 15
31-PPL5-sample16.CEL R S 16 16
32-PPL5-sample17.CEL C S 16 16
33-PPL1-sample02.CEL R E 1 17
34-PPL1-sample03.CEL C E 1 17
35-PPL6-sample02.CEL R E 2 18
36-PPL6-sample03.CEL C E 2 18
37-PPL1-sample04.CEL R E 3 19
38-PPL1-sample05.CEL C E 3 19
39-PPL6-sample04.CEL R E 4 20
40-PPL6-sample05.CEL C E 4 20
41-PPL1-sample06.CEL R E 5 21
42-PPL1-sample07.CEL C E 5 21
43-PPL6-sample06.CEL R E 6 22
44-PPL6-sample07.CEL C E 6 22
45-PPL1-sample08.CEL R E 7 23
46-PPL1-sample09.CEL C E 7 23
47-PPL6-sample08.CEL R E 8 24
48-PPL6-sample09.CEL C E 8 24
49-PPL1-sample10.CEL R E 9 25
50-PPL1-sample11.CEL C E 9 25
51-PPL6-sample10.CEL R E 10 26
52-PPL6-sample11.CEL C E 10 26
53-PPL1-sample12.CEL R E 11 27
54-PPL1-sample13.CEL C E 11 27
55-PPL6-sample12.CEL R E 12 28
56-PPL6-sample13.CEL C E 12 28
57-PPL1-sample14.CEL R E 13 29
58-PPL1-sample15.CEL C E 13 29
59-PPL6-sample14.CEL R E 14 30
60-PPL6-sample15.CEL C E 14 30
61-PPL1-sample16.CEL R E 15 31
62-PPL1-sample17.CEL C E 15 31
63-PPL6-sample16.CEL R E 16 32
64-PPL6-sample17.CEL C E 16 32
65-PPL2-sample02.CEL R L 1 33
66-PPL2-sample03.CEL C L 1 33
67-PPL4-sample02.CEL R L 2 34
68-PPL4-sample03.CEL C L 2 34
69-PPL2-sample04.CEL R L 3 35
70-PPL2-sample05.CEL C L 3 35
71-PPL4-sample04.CEL R L 4 36
72-PPL4-sample05.CEL C L 4 36
73-PPL2-sample06.CEL R L 5 37
74-PPL2-sample07.CEL C L 5 37
75-PPL4-sample06.CEL R L 6 38
76-PPL4-sample07.CEL C L 6 38
77-PPL2-sample08.CEL R L 7 39
78-PPL2-sample09.CEL C L 7 39
79-PPL4-sample08.CEL R L 8 40
80-PPL4-sample09.CEL C L 8 40
81-PPL2-sample10.CEL R L 9 41
82-PPL2-sample11.CEL C L 9 41
83-PPL4-sample10.CEL R L 10 42
84-PPL4-sample11.CEL C L 10 42
85-PPL2-sample12.CEL R L 11 43
86-PPL2-sample13.CEL C L 11 43
87-PPL4-sample12.CEL R L 12 44
88-PPL4-sample13.CEL C L 12 44
89-PPL2-sample14.CEL R L 13 45
90-PPL2-sample15.CEL C L 13 45
91-PPL4-sample14.CEL R L 14 46
92-PPL4-sample15.CEL C L 14 46
93-PPL2-sample16.CEL R L 15 47
94-PPL2-sample17.CEL C L 15 47
95-PPL4-sample16.CEL R L 16 48
96-PPL4-sample17.CEL C L 16 48
--
Karl Brand <k.brand at erasmusmc.nl>
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
lab +31 (0)10 704 3409 fax +31 (0)10 704 4743 mob +31 (0)642 777 268
More information about the Bioconductor
mailing list