[BioC] Parameter names must by syntactically valid names in R

[Seth Falcon]

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