2018-08-19

在运行rsem-to-matrix是会出现R读取文件错误

/home/zz/miniconda3/opt/trinity-2.5.1/util/support_scripts/run_TMM_scale_matrix.pl --matrix genes.isoform.TPM.not_cross_norm > genes.isoform.TMM.EXPR.matrixCMD: R --vanilla -q < __tmp_runTMM.R 1>&2
> library(edgeR)
载入需要的程辑包：limma
>
> rnaseqMatrix = read.table("genes.isoform.TPM.not_cross_norm", header=T, row.names=1, com='', check.names=F)
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  16行没有10元素
Calls: read.table -> scan
停止执行
Error, cmd: R --vanilla -q < __tmp_runTMM.R 1>&2  died with ret (256)  at /home/zz/miniconda3/opt/trinity-2.5.1/util/support_scripts/run_TMM_scale_matrix.pl line 105.
Error, CMD: /home/zz/miniconda3/opt/trinity-2.5.1/util/support_scripts/run_TMM_scale_matrix.pl --matrix genes.isoform.TPM.not_cross_norm > genes.isoform.TMM.EXPR.matrix died with ret 5632 at /home/zz/miniconda3/bin/abundance_estimates_to_matrix.pl line 383.

下面是在网上找的答案R语言读取文件错误

> otu=read.table("otu_table.txt",header=F) Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 2 did not have 26 elements
更改为
> otu=read.table("otu_table.txt",sep="\t",header=T)
正确读入数据

所以将 /home/zz/miniconda3/opt/trinity-2.5.1/util/support_scripts/run_TMM_scale_matrix.pl 的74行添加 sep="\t"

这样不行，可能是合并的文件有问题

使用不当导致环境变量被conda污染