I am using DESeq2 to find deferentially expressed genes from count tables. This is my first time doing it, so I’m a little (a lot) confuse.
My Input files are feature counts generated using featurecounts
I had originally 12 samples (7 treatment and 5 control), first using HISAT2 I performed alignment, then counted the features of gene expression using featurecounts.
Now I am using DESeq2 to determine differentially expressed features. In factor 1 I have named as treatment and selected the colection of feature count output for 7 samples and factor 2 named as control and selected the colection of feature count output for 5 samples.
I am getting two following error (because I did the test two times)
FIRST
error
An error occurred with this dataset:
primary factor: Efecto_carne
DESeq2 run information
sample table:
Efecto_carne
featureCounts on data 117: Counts Tratamiento
featureCounts on data 116: Counts Tratamiento
featureCounts on data
SECOND
error
An error occurred with this dataset:
primary factor: Efecto_carne
Error in DESeqDataSet(se, design = design, ignoreRank) :
some values in assay are negative
Calls: get_deseq_dataset … DESeqDataSetFromHTSeqCount -> DESeqDataSetFromMatrix -> DESeqDataSet