Entering edit mode
Yannick Wurm
▴
220
@yannick-wurm-2314
Last seen 10.2 years ago
Hi,
I just stumbled onto an error creating contrasts in limma 2.12 on R
2.6.2, but could not find it in the mailing list archives or google,
so I thought I might share it for the next person.
Here's what happened:
> cont.matrix= makeContrasts(MT_3hvsMT_0h=
(M_A3h+M_D3h+M_G3h+M_K3h-
(M_A0h+M_D0h+M_G0h+M_K0h))/4, levels=design)
Error in makeContrasts(MT_3hvsMT_0h = (M_A3h + M_D3h + M_G3h +
M_K3h
- :
Parameter names must by syntactically valid names in R
But my same command had worked on a reduced dataset just a few days
earlier.
Turns out the issue came from my targets file:
> cont.matrix= makeContrasts(MT_3hvsMT_0h=
(M_A3h+M_D3h+M_G3h+M_K3h-
(M_A0h+M_D0h+M_G0h+M_K0h))/4, levels=colnames(design)[1:186])
#this one worked
> cont.matrix= makeContrasts(MT_3hvsMT_0h=
(M_A3h+M_D3h+M_G3h+M_K3h-
(M_A0h+M_D0h+M_G0h+M_K0h))/4, levels=colnames(design)[1:187])
Error in makeContrasts(MT_3hvsMT_0h = (M_A3h + M_D3h +
M_G3h +
M_K3h - :
Parameter names must by syntactically valid names in
R
> colnames(design)[187]
[1] "W_P48h "
One of the sample names had spaces in it...
Have a great day,
yannick