[BioC] edgeR glmFit
Jahn Davik [guest]
guest at bioconductor.org
Wed Dec 18 11:21:07 CET 2013
I am working my way through the edgeR User's Guide and following section 3.3, I encounter a problem. I run the following commands - using my own counts data:
## Chapt 3.3 i Users Guide
cots<-read.table("H:/bip1/RNAseq/Data/transcriptsRed.counts.matrix",header=T)
head(cots)
data = as.matrix(cots);
y = round(data);
head(y)
dim(data)
targets<-read.table("H:/bip1/RNAseq/Data/targets.txt",header=T)
targets
# setting up a combined factor
Group<-factor(paste(targets$Treat,targets$Time,sep="."))
cbind(targets,Group=Group)
design<-model.matrix(~0+Group)
colnames(design)<-levels(Group)
design
fit<-glmFit(y,design)
sessionInfo()
Resulting in 'Error in glmFit.default(y, design) : No dispersion values provided.'
I do not quite see where my mistake is and would appreciate help.
Thank you.
jahn
-- output of sessionInfo():
cots<-read.table("H:/bip1/RNAseq/Data/transcriptsRed.counts.matrix",header=T)
> head(cots)
E00R1 E00R2 E00R3 E01R1 E01R2 E01R3 E05R1 E05R2 E05R3 E48R2 E48R3 E96R1 E96R2 E96R3 J00R1 J00R2 J00R3 J01R1
comp168996_c1_seq1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
comp442719_c0_seq1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
comp436057_c0_seq13 0.00 7.38 21.04 0.00 0.00 0.21 21.65 0.00 0.00 0.00 0.86 0.57 9.69 18.73 0.00 0.00 0.00 7.14
comp415319_c0_seq20 28.17 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
comp428135_c0_seq8 249.73 228.53 172.18 57.52 104.48 113.96 187.05 94.64 84.65 134.65 99.82 0.00 65.46 82.83 219.37 59.18 134.04 81.56
comp73458_c0_seq1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
J01R2 J01R3 J05R1 J05R2 J05R3 J48R2 J48R3 J96R1 J96R2 J96R3
comp168996_c1_seq1 1.00 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
comp442719_c0_seq1 0.00 0.00 35.09 0.00 0.00 0.00 0 0.00 0.00 0.00
comp436057_c0_seq13 3.07 0.00 0.05 0.00 0.00 19.09 0 0.60 0.00 0.00
comp415319_c0_seq20 0.00 0.00 0.00 0.00 0.00 0.00 0 0.00 0.00 0.00
comp428135_c0_seq8 87.00 188.03 177.74 115.65 75.66 26.50 0 41.02 131.62 101.48
comp73458_c0_seq1 0.00 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00 0.00
> data = as.matrix(cots);
> y = round(data);
> head(y)
E00R1 E00R2 E00R3 E01R1 E01R2 E01R3 E05R1 E05R2 E05R3 E48R2 E48R3 E96R1 E96R2 E96R3 J00R1 J00R2 J00R3 J01R1 J01R2
comp168996_c1_seq1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
comp442719_c0_seq1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
comp436057_c0_seq13 0 7 21 0 0 0 22 0 0 0 1 1 10 19 0 0 0 7 3
comp415319_c0_seq20 28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
comp428135_c0_seq8 250 229 172 58 104 114 187 95 85 135 100 0 65 83 219 59 134 82 87
comp73458_c0_seq1 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0
J01R3 J05R1 J05R2 J05R3 J48R2 J48R3 J96R1 J96R2 J96R3
comp168996_c1_seq1 0 1 0 0 0 0 0 0 0
comp442719_c0_seq1 0 35 0 0 0 0 0 0 0
comp436057_c0_seq13 0 0 0 0 19 0 1 0 0
comp415319_c0_seq20 0 0 0 0 0 0 0 0 0
comp428135_c0_seq8 188 178 116 76 26 0 41 132 101
comp73458_c0_seq1 1 0 0 0 0 0 0 0 0
>
> dim(data)
[1] 621694 28
>
> targets<-read.table("H:/bip1/RNAseq/Data/targets.txt",header=T)
> targets
Sample Treat Time
1 E00R1 Els 00h
2 E00R2 Els 00h
3 E00R3 Els 00h
4 E01R1 Els 01h
5 E01R2 Els 01h
6 E01R3 Els 01h
7 E05R1 Els 05h
8 E05R2 Els 05h
9 E05R3 Els 05h
10 E48R2 Els 48h
11 E48R3 Els 48h
12 E96R1 Els 96h
13 E96R2 Els 96h
14 E96R3 Els 96h
15 J00R1 Jon 00h
16 J00R2 Jon 00h
17 J00R3 Jon 00h
18 J01R1 Jon 01h
19 J01R2 Jon 01h
20 J01R3 Jon 01h
21 J05R1 Jon 05h
22 J05R2 Jon 05h
23 J05R3 Jon 05h
24 J48R2 Jon 48h
25 J48R3 Jon 48h
26 J96R1 Jon 96h
27 J96R2 Jon 96h
28 J96R3 Jon 96h
>
> # setting up a combined factor
>
> Group<-factor(paste(targets$Treat,targets$Time,sep="."))
> cbind(targets,Group=Group)
Sample Treat Time Group
1 E00R1 Els 00h Els.00h
2 E00R2 Els 00h Els.00h
3 E00R3 Els 00h Els.00h
4 E01R1 Els 01h Els.01h
5 E01R2 Els 01h Els.01h
6 E01R3 Els 01h Els.01h
7 E05R1 Els 05h Els.05h
8 E05R2 Els 05h Els.05h
9 E05R3 Els 05h Els.05h
10 E48R2 Els 48h Els.48h
11 E48R3 Els 48h Els.48h
12 E96R1 Els 96h Els.96h
13 E96R2 Els 96h Els.96h
14 E96R3 Els 96h Els.96h
15 J00R1 Jon 00h Jon.00h
16 J00R2 Jon 00h Jon.00h
17 J00R3 Jon 00h Jon.00h
18 J01R1 Jon 01h Jon.01h
19 J01R2 Jon 01h Jon.01h
20 J01R3 Jon 01h Jon.01h
21 J05R1 Jon 05h Jon.05h
22 J05R2 Jon 05h Jon.05h
23 J05R3 Jon 05h Jon.05h
24 J48R2 Jon 48h Jon.48h
25 J48R3 Jon 48h Jon.48h
26 J96R1 Jon 96h Jon.96h
27 J96R2 Jon 96h Jon.96h
28 J96R3 Jon 96h Jon.96h
>
> design<-model.matrix(~0+Group)
> colnames(design)<-levels(Group)
> design
Els.00h Els.01h Els.05h Els.48h Els.96h Jon.00h Jon.01h Jon.05h Jon.48h Jon.96h
1 1 0 0 0 0 0 0 0 0 0
2 1 0 0 0 0 0 0 0 0 0
3 1 0 0 0 0 0 0 0 0 0
4 0 1 0 0 0 0 0 0 0 0
5 0 1 0 0 0 0 0 0 0 0
6 0 1 0 0 0 0 0 0 0 0
7 0 0 1 0 0 0 0 0 0 0
8 0 0 1 0 0 0 0 0 0 0
9 0 0 1 0 0 0 0 0 0 0
10 0 0 0 1 0 0 0 0 0 0
11 0 0 0 1 0 0 0 0 0 0
12 0 0 0 0 1 0 0 0 0 0
13 0 0 0 0 1 0 0 0 0 0
14 0 0 0 0 1 0 0 0 0 0
15 0 0 0 0 0 1 0 0 0 0
16 0 0 0 0 0 1 0 0 0 0
17 0 0 0 0 0 1 0 0 0 0
18 0 0 0 0 0 0 1 0 0 0
19 0 0 0 0 0 0 1 0 0 0
20 0 0 0 0 0 0 1 0 0 0
21 0 0 0 0 0 0 0 1 0 0
22 0 0 0 0 0 0 0 1 0 0
23 0 0 0 0 0 0 0 1 0 0
24 0 0 0 0 0 0 0 0 1 0
25 0 0 0 0 0 0 0 0 1 0
26 0 0 0 0 0 0 0 0 0 1
27 0 0 0 0 0 0 0 0 0 1
28 0 0 0 0 0 0 0 0 0 1
attr(,"assign")
[1] 1 1 1 1 1 1 1 1 1 1
attr(,"contrasts")
attr(,"contrasts")$Group
[1] "contr.treatment"
>
> fit<-glmFit(y,design)
Error in glmFit.default(y, design) : No dispersion values provided.
>
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=Norwegian (Bokmål)_Norway.1252 LC_CTYPE=Norwegian (Bokmål)_Norway.1252 LC_MONETARY=Norwegian (Bokmål)_Norway.1252
[4] LC_NUMERIC=C LC_TIME=Norwegian (Bokmål)_Norway.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] edgeR_3.4.2 limma_3.18.6 DESeq_1.14.0 lattice_0.20-24 locfit_1.5-9.1 Biobase_2.22.0 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] annotate_1.40.0 AnnotationDbi_1.24.0 DBI_0.2-7 genefilter_1.44.0 geneplotter_1.40.0 grid_3.0.2
[7] IRanges_1.20.6 RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 survival_2.37-4
[13] tools_3.0.2 XML_3.98-1.1 xtable_1.7-1
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