Hi, all

I am trying to use goseq for RNAseq data analysis of a non-native bacteria,
I fetch the genelength data and GO term data by using ensembl Perl API.
Differential expression was done by DESeq2.

After data run pwf of goseq, error occurred as following:

###

Error in if (hi <= low) { : missing value where TRUE/FALSE needed

Have any one met this before?

How could I solved this problem?

Thanks!



My workflow were as following

##   import the genes ID which I fetch from Ensembl

HZ254gene_data <- read.delim("E:/HZ_GO_enrichment/HZ254gene_data.txt",
quote="")

colnames(HZ254gene_data)[1]="locus_tag"



##  get assayed gene vector

assayed.genes=HZ254gene_data$locus_tag

assayed.genes1=as.vector(assayed.genes)

is.vector(assayed.genes1)

[1] TRUE

head (assayed.genes1)

[1] "Mtc_0001" "Mtc_0002" "Mtc_0003" "Mtc_0004" "Mtc_0005" "Mtc_0006"

str(assayed.genes1)

chr [1:2512] "Mtc_0001" "Mtc_0002" "Mtc_0003" "Mtc_0004" "Mtc_0005" ...





## get gene length data for pwf bias.data

length=HZ254gene_data$length

is.vector(length)

[1] TRUE

names(length)=assayed.genes1

head(length)

Mtc_0001 Mtc_0002 Mtc_0003 Mtc_0004 Mtc_0005 Mtc_0006

     768      654     1899     1770      351      654

#

str(length)

 Named int [1:2512] 768 654 1899 1770 351 654 903 72 966 1071 ...

 - attr(*, "names")= chr [1:2512] "Mtc_0001" "Mtc_0002" "Mtc_0003"
"Mtc_0004" ...







##import results from DESeq2 and get the DEgenes

HZ254DifList_Mer <- read.delim("E:/HZ_GO_enrichment/HZ254DifList_Mer.txt")

de.genes1=as.integer(HZ254DifList_Mer$padj<0.05)



##get the genes for pwf

gene.vector=as.integer(de.genes1)

names(gene.vector)=assayed.genes1

head(gene.vector)



##import the GO_gene association table from ensembl API

HZ254gene_go <- read.delim("E:/HZ_GO_enrichment/HZ254gene_go.txt", quote="")

go.terms=HZ254gene_go





## run pwf,

pwf=nullp(gene.vector,bias.data=length)

##got errors

Error in if (hi <= low) { : missing value where TRUE/FALSE needed



sessionInfo()

R version 3.0.2 (2013-09-25)

Platform: x86_64-w64-mingw32/x64 (64-bit)



locale:

[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936

[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936

[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936

[4] LC_NUMERIC=C

[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936



attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base



other attached packages:

[1] goseq_1.14.0            geneLenDataBase_0.99.12 BiasedUrn_1.06.1

[4] BiocInstaller_1.12.0



loaded via a namespace (and not attached):

 [1] AnnotationDbi_1.24.0   Biobase_2.22.0         BiocGenerics_0.8.0

 [4] biomaRt_2.18.0         Biostrings_2.30.1      bitops_1.0-6

 [7] BSgenome_1.30.0        DBI_0.2-7              GenomicFeatures_1.14.2

[10] GenomicRanges_1.14.4   grid_3.0.2             IRanges_1.20.6

[13] lattice_0.20-24        Matrix_1.1-2           mgcv_1.7-28

[16] nlme_3.1-113           parallel_3.0.2         RCurl_1.95-4.1

[19] Rsamtools_1.14.3       RSQLite_0.11.4         rtracklayer_1.22.3

[22] stats4_3.0.2           tools_3.0.2            XML_3.98-1.1

[25] XVector_0.2.0          zlibbioc_1.8.0

-- 
Pengfei Liu, PhD Candidate
Lab of Molecular Ecology - Max Planck Partner Group
College of Resources and Environmental Sciences
China Agricultural University
No.2 Yuanmingyuanxilu, Beijing, 100193
P.R. China

Tel: +86-10-62731358
Fax: +86-10-62731016

E-mail: liupfskygre@gmail.com

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