Parameter names must by syntactically valid names in R
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k. brand ▴ 420
@k-brand-1874
Last seen 9.9 years ago
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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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 9.9 years ago
Hi Karl, On 2/1/10 8:54 AM, Karl Brand wrote: => Anyone that could shed light on the error- > > "Parameter names must by syntactically valid names in R" <snip> > 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. Hmm, that part is curious, but I don't think we have enough information to comment usefully. <snip> > > 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" Those last two do not look like valid names to me. The ":" is not allowed in naked identifiers in R. You could try converting the ":" to "." or "_". Perhaps: colnames(design) <- sub(":", "_", colnames(design)) HTH, + seth -- Seth Falcon Bioconductor Core Team | FHCRC
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Thank you Seth, On 2/1/2010 6:51 PM, Seth Falcon wrote: > Hi Karl, > > On 2/1/10 8:54 AM, Karl Brand wrote: > => Anyone that could shed light on the error- >> >> "Parameter names must by syntactically valid names in R" > > <snip> > >> 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. > > Hmm, that part is curious, but I don't think we have enough information > to comment usefully. My bad: looks like some one (definitely not me, uhuh...) changed the code in the intervening period. > <snip> >> > 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" > > Those last two do not look like valid names to me. The ":" is not > allowed in naked identifiers in R. I didn't know this. Strange (to me) that R outputs these identifiers for the columns with interaction; which obviously need relabeling. > You could try converting the ":" to "." or "_". Perhaps: > > colnames(design) <- sub(":", "_", colnames(design)) Worked a charm, though i did get this warning: Warning message: In contrasts.fit(fit, cont.matrix) : row names of contrasts don't match col names of coefficients So tried: > rownames(contrasts) <- colnames(coefficients) Which appear's to solve the problem (even though i dont realise the extent of the consequences of this action the output looked about right). Another disgruntled biologist assuaged. Big cheers, Karl > HTH, > > + seth > -- 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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