I am having issues with DESeq2. I get this error message
Fatal error: An undefined error occurred, please check your input carefully and contact your administrator.
Import genomic features from the file as a GRanges object … OK
Prepare the ‘metadata’ data frame … OK
Make the TxDb object … OK
‘select()’ returned 1:many mapping between keys and columns
abundance.h5 is typically faster than
reading in files with read.delim (install ‘readr’ package for speed up)
1 2 3 4 5 6
using counts and average transcript lengths from tximport
In .get_cds_IDX(type, phase) :
The “phase” metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
estimating size factors
using ‘avgTxLength’ from assays(dds), correcting for library size
gene-wise dispersion estimates
Error in estimateDispersionsFit(object, fitType = fitType, quiet = quiet) :
all gene-wise dispersion estimates are within 2 orders of magnitude
from the minimum value, and so the standard curve fitting techniques will not work.
One can instead use the gene-wise estimates as final estimates:
dds <- estimateDispersionsGeneEst(dds)
dispersions(dds) <- mcols(dds)$dispGeneEst
…then continue with testing using nbinomWaldTest or nbinomLRT
Calls: DESeq … estimateDispersions -> .local -> estimateDispersionsFit
I’m not exactly sure what to do to remedy this problem.