Thanks for your explanations!
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Goseq: Pwf: Error In If (Hi <= Low) { : Missing Value Where True/False Needed
Hi, all
Dose anyone familiar with the use of goseq package here, I always get quick reply here, so I post my questions here, hope for some suggestions.
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
It seems to be the problem of the names or ID problem, but I could not solved it till now.
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
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liupfskygre
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liupfskygre
4 answers
To not leave this question appear unanswered:
The first thing you have do after seeing such an error is to call traceback() and add the output to the error report.
Error in if (hi <= low) { : missing value where TRUE/FALSE needed
means, as it says, there is a missing value where if requires a TRUE/FALSE value, <= and other comparison operators in R
yield 'NA' if and only if at least one of the values is missing itself. In conclusion, your input data contains missing values which
goseq does not handle.
In case that happens, missing values need to be removed (e.g. by using complete.cases) or imputed, see http://www.statmethods.net/input/missingdata.html
for a quick tutorial.
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Michael Dondrup
de.genes1=as.integer(HZ254DifList_Mer$padj<0.05)`
This looks like a logical vector casted into an integer - can you print de.genes1 out
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Jeremy Leipzig
thanks, as for my case, missing data "NA" in the de.genes1 caused the problem! At first I tried to convert de.gene1 into numeric, but failed, recheck the data found NA existed.
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liupfskygre
In case anyone else runs into this problem, one way you can end up with the same error is if the gene lengths are all the same.
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keith.hughitt
I had the same error message and in my case it a binary vector had NAs, so basically:
> genes = as.integer(DESeqoutput$padj <= 0.05 & > !is.na(DESeqoutput$padj)) # Give all values less than 0.05 and no NAs
However, when I call for nullp() I get following warning:
Can't find mm10/ensGene length data in genLenDataBase...
Found the annotaion package, TxDb.Mmusculus.UCSC.mm10.ensGene
Trying to get the gene lengths from it.
Warning messages:
1: In library() : library ‘/usr/lib/R/site-library’ contains no packages
2: In pcls(G) : initial point very close to some inequality constraints
It is warning message but I would like to interpret it. What does it mean? Thanks
that R is gibberish. What do you think the gene vector should look like?
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Jeremy Leipzig
Show us what genes looks like after your faulty code above.
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Jeremy Leipzig
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Hi, liupfskygre, It's hard to know exactly what the issue is without a reproducible example, but perhaps the assignment of values to variable names, which are also base R functions, could be a problem. Try replacing
length=HZ254gene_data$lengthwithlgth=HZ254gene_data$length. If thenullpfunction callslength(the function), your use of this name as a variable might be a conflict.thanks for your reminding! I recheck the data and found where the problems is, there were some genes in the dataset that do not have expression data, which were assigned as NA!