Hello, I’m trying to do GO analysis using goseq but I get this error:
<<Warning message:
In pcls(G) : initial point very close to some inequality constraints
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: paral>>
as input I had this:
To add more details :
Details
Execution resulted in the following messages:
Fatal error: An undefined error occured, please check your input carefully and contact your administrator.
Tool generated the following standard error:
Warning message:
In pcls(G) : initial point very close to some inequality constraints
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:dplyr’:
combine, intersect, setdiff, union
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:dplyr’:
first, rename
The following object is masked from ‘package:base’:
expand.grid
Attaching package: ‘IRanges’
The following objects are masked from ‘package:dplyr’:
collapse, desc, slice
Attaching package: ‘AnnotationDbi’
The following object is masked from ‘package:dplyr’:
select
Using manually entered categories.
Error in [.default(summary(map), , 1) : incorrect number of dimensions
Calls: goseq → reversemapping → [ → [.table → NextMethod
Any help would be much appreciated.
edit: from what I noticed, the order of the genes in the two inputs(Gene IDs and differential expression, and Gene IDs and length) is different , could this be the problem? and if yes, how can I edit them so both inputs have the same order of genes? edit2: I saw a video on YouTube where the genes on the two inputs had different order and it still worked
