RNAseq有参转录组分析差异表达分析免疫亚型之间差异表达这一环节出现以下问题

#, S1 为免疫侵润高组 DESeq2

Rscript $scriptdir/deseq_analysis1.r -i $workdir/4.expression/all_gene_count.tsv \

--fdr 0.01 --fc 2 -m normal_vs_tumor.compare.txt -t group\

--case tumor --control normal -p normal_vs_tumor.deseq

#免疫亚型之间差异表达, S1 为免疫侵润高组 edgeR

Rscript $scriptdir/edger_analysis1.r -i $workdir/4.expression/all_gene_count.tsv \

--fdr 0.01 --fc 2 -m normal_vs_tumor.compare.txt -t group\

--case tumor --control normal -p normal_vs_tumor.edger

deseq2运行成功，edger运行失败

(rnaseq) [yangxm@sonmi 5.deg]$ Rscript $scriptdir/edger_analysis1.r -i $workdir/4.expression/all_gene_count.tsv \

--fdr 0.01 --fc 2 -m normal_vs_tumor.compare.txt -t group\

--case tumor --control normal -p normal_vs_tumor.edger

Warning: The system is configured to read the RTC time in the local time zone.

This mode cannot be fully supported. It will create various problems

with time zone changes and daylight saving time adjustments. The RTC

time is never updated, it relies on external facilities to maintain it.

If at all possible, use RTC in UTC by calling

'timedatectl set-local-rtc 0'.

[1] "abstract_factors is over"

[1] "read count data ..."

[1] "read count data is over"

Disp = 0.00232 , BCV = 0.0481

Error in decideTestsDGE(et, adjust.method = "BH", p.value = fdr, lfc = log2(fold_change)) :

could not find function "decideTestsDGE"

Execution halted

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