[R] BioConductor package: 'oligo'

Sun Oct 7 22:13:24 CEST 2012

Hi Franklin,

As you note, this is a bioconductor package, and they have a separate
mailing list for support (fully of terribly knowledgeable and
responsive folks) I know it's somewhat unpleasant to be told to look
elsewhere after you've spent a good amount of time on it already, but
I think it's worth your time to repost to that list:
http://www.bioconductor.org/help/mailing-list/mailform/

Cheers,
Michael

On Sun, Oct 7, 2012 at 5:22 PM, Johnson, Franklin Theodore
<franklin.johnson at email.wsu.edu> wrote:
> Dear Help,
>
>
>
> After loading the pd.Citrus library and checking the DataFrame, I ran
>> the R code for:
>>
>> 1) 'oligo'
>>
>>
>>
>> {> library(pd.citrus)
>> Loading required package: RSQLite
>> Loading required package: DBI
>> > data(pmSequence)
>>
>> > show(pmSequence)
>> DataFrame with 341730 rows and 2 columns
>> fid sequence
>> <integer> <DNAStringSet>
>> 1 990 GCTTTTGGAACGATGGCGATGGCTA
>> 2 991 CGACGGGTTGCCTTCGGAGCTAAAT
>> 3 992 TACTGCAGAAGACCATTACCCTACA
>> 4 993 TCACATAGCTGTGCAAGGACCGTAT
>> 5 994 TCGCCTAGCAAAGCTGCCAGCATGT
>> 6 995 TTACGTCTACGTGGTGGTGCTAAGA
>> 7 996 CCGAACGACCTGTTGGACCAAAGCA
>> 8 999 AAGCTAGTCTAGCTCCACCGACGGC
>> 9 1000 TTTTCACCGGTGACGTGCCGGTCGC
>> ... ... ...
>> 341722 963599 AAATTCGACATTTTCTTTACTGAGA
>> 341723 963790 GGATGCCCTCCGGTAATTGAATCAT
>> 341724 963802 GTTCAGCTCAAACCCTACATAGAGA
>> 341725 963818 GGAAAAATGTCTCAACCAGCTGGTT
>> 341726 963841 GAGAAGATGTTCAGAGGGCCCTACA
>> 341727 963859 GGTGCAGTTCGACTCTAAGTTTGCT
>> 341728 963863 AAACACGGTTATTCATCTGCGAAAC
>> 341729 963874 GATGCTCTTCATTGGGAGGCAGCGA
>> 341730 963889 ATTGATACAGCCTTCTCTGCAGTAA
>> > getwd()
>> [1] "C:/Users/franklin.johnson.PW50-WEN/Desktop/GSE33964_citrus epi
>> cells/exData"}
>>
>> {library(oligo)
>> > celFiles<-list.celfiles("exData", full.names=TRUE)
>> > affyCit<-read.celfiles("GSM839728_GF_28mm_EC-1.CEL",
>> "GSM839729_GF_28mm_EC-2.CEL", "GSM839730_GF_28mm_EC-3.CEL",
>> "GSM839731_GF_28mm_PC-1.CEL", "GSM839732_GF_28mm_PC-2.CEL",
>> "GSM839733_GF_28mm_PC-3.CEL", "GSM839734_GF_41mm_EC-1.CEL",
>> "GSM839735_GF_41mm_EC-2.CEL", "GSM839736_GF_41mm_EC-3.CEL",
>> "GSM839737_GF_41mm_PC-1.CEL", "GSM839738_GF_41mm_PC-2.CEL",
>> "GSM839739_GF_41mm_PC-3.CEL", pkgname="pd.citrus")
>> Platform design info loaded.
>> Reading in : GSM839728_GF_28mm_EC-1.CEL
>> Reading in : GSM839729_GF_28mm_EC-2.CEL
>> Reading in : GSM839730_GF_28mm_EC-3.CEL
>> Reading in : GSM839731_GF_28mm_PC-1.CEL
>> Reading in : GSM839732_GF_28mm_PC-2.CEL
>> Reading in : GSM839733_GF_28mm_PC-3.CEL
>> Reading in : GSM839734_GF_41mm_EC-1.CEL
>> Reading in : GSM839735_GF_41mm_EC-2.CEL
>> Reading in : GSM839736_GF_41mm_EC-3.CEL
>> Reading in : GSM839737_GF_41mm_PC-1.CEL
>> Reading in : GSM839738_GF_41mm_PC-2.CEL
>> Reading in : GSM839739_GF_41mm_PC-3.CEL
>> > pmSeq<-pmSequence(affyCit)
>> > pmSeq[1:10]
>> A DNAStringSet instance of length 10
>> width seq
>> [1] 25 GCTTTTGGAACGATGGCGATGGCTA
>> [2] 25 CGACGGGTTGCCTTCGGAGCTAAAT
>> [3] 25 TACTGCAGAAGACCATTACCCTACA
>> [4] 25 TCACATAGCTGTGCAAGGACCGTAT
>> [5] 25 TCGCCTAGCAAAGCTGCCAGCATGT
>> [6] 25 TTACGTCTACGTGGTGGTGCTAAGA
>> [7] 25 CCGAACGACCTGTTGGACCAAAGCA
>> [8] 25 AAGCTAGTCTAGCTCCACCGACGGC
>> [9] 25 TTTTCACCGGTGACGTGCCGGTCGC
>> [10] 25 GGTTAAGCCCGGCACTATCCGGGCA
>> > pmsLog2<-log2(pm(affyCit))
>> > plot(pmsLog2) #the plots looks good across arrays (object=affyCit)
>>
>> However, still get:
>> > coefs<-getAffinitySplineCoefficients(pmsLog2, pmSeq)
>> Error in model.frame.default(formula = intensities ~ design,
>> drop.unused.levels = TRUE) :
>> variable lengths differ (found for 'design')
>
>
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> 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] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] oligo_1.22.0        Biobase_2.18.0      oligoClasses_1.20.0
> [4] BiocInstaller_1.8.1 BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>  [1] affxparser_1.30.0     affyio_1.26.0         Biostrings_2.26.1
>  [4] bit_1.1-8             codetools_0.2-8       DBI_0.2-5
>  [7] ff_2.2-7              foreach_1.4.0         GenomicRanges_1.10.1
> [10] IRanges_1.16.2        iterators_1.0.6       parallel_2.15.1
> [13] preprocessCore_1.20.0 splines_2.15.1        stats4_2.15.1
> [16] tools_2.15.1          zlibbioc_1.4.0
>
> I have been working on the issue for two weeks already.
>
> For example, above I loaded the Citrus.pd, additionally, I tried working with library(citruscdf), although this did not work either?
>
> Moreover, I used R 2.6 with the devel 'affyio' package version 1.27.1, but cannot run 'oligo' with R 2.6 for some reason (i.e. error in list.celFiles and read.celfiles commands), although R version for 'oligo' is 2.15 or greater, so cannot use the list matrix generated in 'affyio' version 1.27 on R 2.6 cause is does not seem compatible with 'oligo' version 1.22 on R 2.6. I am also using the recently updated BioC version 2.11.
>
> In oligo using R v. 2.15, I am able to view the .CEL images, make boxplots, MAplots of the data, but cannot proceed beyond this point (as indicated above).
>
>
>
> In summary, is this a bug in the 'oligo' package??
>
>
>
> Any assistance is greatly appreciated.
>
> If you have questions or need additional information, please feel free to contact me.
>
>
>
> Best Regards,
>
>
>
> Franklin
>