[BioC] Parameter names must by syntactically valid names in R
Karl Brand
k.brand at erasmusmc.nl
Mon Feb 1 17:54:05 CET 2010
Dear BioCers,
Anyone that could shed light on the error-
"Parameter names must by syntactically valid names in R"
-would be greatly appreciated.
Google turned up were these relevant findings:
https://stat.ethz.ch/pipermail/bioconductor/2008-March/021440.html
-which suggested spaces in names could yield such errors. I failed to
find such spaces in my targets file (fwd at bottom).
http://rss.acs.unt.edu/Rdoc/library/base/html/make.names.html
-indicated names should not begin with numbers or ".". Which they do not
as far a i could find, atleast in my targets or sript.
Of particular note is that identical code run 24 hrs earlier on a
different machine succeeded without this error. Unfortunately i do not
have sessionInfo from that session and wont be able gain it as such any
time soon.
What am i doing wrong (today and not yesterday!)?
Look forward to any thoughts on this, cheers,
Karl
> targets <-
read.delim("RNA_Targets_RE-ORDered&timeInRank&NoAnimal_L-E-S_c.txt")
> Tissue <- factor(targets$Tissue)
> Pperiod <- factor(targets$Pperiod)
> Time <- factor(targets$Time)
> design <- model.matrix(~0 + Tissue*Pperiod + Time, data=targets)
> colnames(design)
[1] "TissueC" "TissueR" "PperiodLO"
[4] "PperiodSH" "Timeb" "Timec"
[7] "Timed" "Timee" "Timef"
[10] "Timeg" "Timeh" "Timei"
[13] "Timej" "Timek" "Timel"
[16] "Timem" "Timen" "Timeo"
[19] "Timep" "TissueR:PperiodLO" "TissueR:PperiodSH"
> fit <- lmFit(rma.pp, design)
> cont.matrix <- makeContrasts(TissueR-TissueC, levels = design)
Error in makeContrasts(TissueR - TissueC, levels = design) :
Parameter names must by syntactically valid names in R
> sessionInfo()
R version 2.10.1 (2009-12-14)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] grDevices datasets splines graphics stats tcltk
[7] utils methods base
other attached packages:
[1] mouse4302cdf_2.5.0 limma_3.2.1 affy_1.24.2
[4] Biobase_2.6.1 svSocket_0.9-48 TinnR_1.0.3
[7] R2HTML_1.59-1 Hmisc_3.7-0 survival_2.35-7
loaded via a namespace (and not attached):
[1] affyio_1.14.0 cluster_1.12.1 grid_2.10.1
[4] lattice_0.17-26 preprocessCore_1.8.0 svMisc_0.9-56
[7] tools_2.10.1
>
Targets file, "RNA_Targets_RE-ORDered&timeInRank&NoAnimal_L-E-S_c.txt":
FileName Tissue Pperiod Time
F01-Karl-Hyb3-PPL3-sample02.CEL R SH a
F02-Karl-Hyb3-PPL3-sample03.CEL C SH a
F03-Karl-Hyb3-PPL5-sample02.CEL R SH b
F04-Karl-Hyb3-PPL5-sample03.CEL C SH b
F05-Karl-Hyb3-PPL3-sample04.CEL R SH c
F06-Karl-Hyb3-PPL3-sample05.CEL C SH c
F07-Karl-Hyb3-PPL5-sample04.CEL R SH d
F08-Karl-Hyb3-PPL5-sample05.CEL C SH d
F09-Karl-Hyb3-PPL3-sample06.CEL R SH e
F10-Karl-Hyb3-PPL3-sample07.CEL C SH e
F11-Karl-Hyb3-PPL5-sample06.CEL R SH f
F12-Karl-Hyb3-PPL5-sample07.CEL C SH f
F13-Karl-Hyb3-PPL3-sample08.CEL R SH g
F14-Karl-Hyb3-PPL3-sample09.CEL C SH g
F15-Karl-Hyb3-PPL5-sample08.CEL R SH h
F16-Karl-Hyb3-PPL5-sample09.CEL C SH h
F17-Karl-Hyb3-PPL3-sample10.CEL R SH i
F18-Karl-Hyb3-PPL3-sample11.CEL C SH i
F19-Karl-Hyb3-PPL5-sample10.CEL R SH j
F20-Karl-Hyb3-PPL5-sample11.CEL C SH j
F21-Karl-Hyb3-PPL3-sample12.CEL R SH k
F22-Karl-Hyb3-PPL3-sample13.CEL C SH k
F23-Karl-Hyb3-PPL5-sample12.CEL R SH l
F24-Karl-Hyb3-PPL5-sample13.CEL C SH l
F25-Karl-Hyb3-PPL3-sample14.CEL R SH m
F26-Karl-Hyb3-PPL3-sample15.CEL C SH m
F27-Karl-Hyb3-PPL5-sample14.CEL R SH n
F28-Karl-Hyb3-PPL5-sample15.CEL C SH n
F29-Karl-Hyb3-PPL3-sample16.CEL R SH o
F30-Karl-Hyb3-PPL3-sample17.CEL C SH o
F31-Karl-Hyb3-PPL5-sample16.CEL R SH p
F32-Karl-Hyb3-PPL5-sample17.CEL C SH p
F33-Karl-Hyb1-PPL1-sample02.CEL R EQ a
F34-Karl-Hyb1-PPL1-sample03.CEL C EQ a
F35-Karl-Hyb1-PPL6-sample02.CEL R EQ b
F36-Karl-Hyb1-PPL6-sample03.CEL C EQ b
F37-Karl-Hyb1-PPL1-sample04.CEL R EQ c
F38-Karl-Hyb1-PPL1-sample05.CEL C EQ c
F39-Karl-Hyb1-PPL6-sample04.CEL R EQ d
F40-Karl-Hyb1-PPL6-sample05.CEL C EQ d
F41-Karl-Hyb1-PPL1-sample06.CEL R EQ e
F42-Karl-Hyb1-PPL1-sample07.CEL C EQ e
F43-Karl-Hyb1-PPL6-sample06.CEL R EQ f
F44-Karl-Hyb1-PPL6-sample07.CEL C EQ f
F45-Karl-Hyb1-PPL1-sample08.CEL R EQ g
F46-Karl-Hyb1-PPL1-sample09.CEL C EQ g
F47-Karl-Hyb1-PPL6-sample08.CEL R EQ h
F48-Karl-Hyb1-PPL6-sample09.CEL C EQ h
F49-Karl-Hyb1-PPL1-sample10.CEL R EQ i
F50-Karl-Hyb1-PPL1-sample11.CEL C EQ i
F51-Karl-Hyb1-PPL6-sample10.CEL R EQ j
F52-Karl-Hyb1-PPL6-sample11.CEL C EQ j
F53-Karl-Hyb1-PPL1-sample12.CEL R EQ k
F54-Karl-Hyb1-PPL1-sample13.CEL C EQ k
F55-Karl-Hyb1-PPL6-sample12.CEL R EQ l
F56-Karl-Hyb1-PPL6-sample13.CEL C EQ l
F57-Karl-Hyb1-PPL1-sample14.CEL R EQ m
F58-Karl-Hyb1-PPL1-sample15.CEL C EQ m
F59-Karl-Hyb1-PPL6-sample14.CEL R EQ n
F60-Karl-Hyb1-PPL6-sample15.CEL C EQ n
F61-Karl-Hyb1-PPL1-sample16.CEL R EQ o
F62-Karl-Hyb1-PPL1-sample17.CEL C EQ o
F63-Karl-Hyb1-PPL6-sample16.CEL R EQ p
F64-Karl-Hyb1-PPL6-sample17.CEL C EQ p
F65-Karl-Hyb2-PPL2-sample02.CEL R LO a
F66-Karl-Hyb2-PPL2-sample03.CEL C LO a
F67-Karl-Hyb2-PPL4-sample02.CEL R LO b
F68-Karl-Hyb2-PPL4-sample03.CEL C LO b
F69-Karl-Hyb2-PPL2-sample04.CEL R LO c
F70-Karl-Hyb2-PPL2-sample05.CEL C LO c
F71-Karl-Hyb2-PPL4-sample04.CEL R LO d
F72-Karl-Hyb2-PPL4-sample05.CEL C LO d
F73-Karl-Hyb2-PPL2-sample06.CEL R LO e
F74-Karl-Hyb2-PPL2-sample07.CEL C LO e
F75-Karl-Hyb2-PPL4-sample06.CEL R LO f
F76-Karl-Hyb2-PPL4-sample07.CEL C LO f
F77-Karl-Hyb2-PPL2-sample08.CEL R LO g
F78-Karl-Hyb2-PPL2-sample09.CEL C LO g
F79-Karl-Hyb2-PPL4-sample08.CEL R LO h
F80-Karl-Hyb2-PPL4-sample09.CEL C LO h
F81-Karl-Hyb2-PPL2-sample10.CEL R LO i
F82-Karl-Hyb2-PPL2-sample11.CEL C LO i
F83-Karl-Hyb2-PPL4-sample10.CEL R LO j
F84-Karl-Hyb2-PPL4-sample11.CEL C LO j
F85-Karl-Hyb2-PPL2-sample12.CEL R LO k
F86-Karl-Hyb2-PPL2-sample13.CEL C LO k
F87-Karl-Hyb2-PPL4-sample12.CEL R LO l
F88-Karl-Hyb2-PPL4-sample13.CEL C LO l
F89-Karl-Hyb2-PPL2-sample14.CEL R LO m
F90-Karl-Hyb2-PPL2-sample15.CEL C LO m
F91-Karl-Hyb2-PPL4-sample14.CEL R LO n
F92-Karl-Hyb2-PPL4-sample15.CEL C LO n
F93-Karl-Hyb2-PPL2-sample16.CEL R LO o
F94-Karl-Hyb2-PPL2-sample17.CEL C LO o
F95-Karl-Hyb2-PPL4-sample16.CEL R LO p
F96-Karl-Hyb2-PPL4-sample17.CEL C LO p
--
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
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