无法从R的sva库运行ComBat脚本 [英] Unable to run ComBat script from R's sva library

问题描述

我试图在具有2个批处理的数据集上运行ComBat脚本，但是由于我是R新手，因此出现错误，并且我不知道如何检查代码.

I am trying to run ComBat script on a dataset with 2 batches, but I am getting errors and I do not know how to inspect code since I am an R newbie.

我以这种方式运行ComBat方法:

I am running ComBat method in this way:

# Load sva
library(sva)
# Read expression values
dat = read.table('dataset.xls', header=TRUE, sep='\t')
# Read sample information file about batches
sif = read.delim('sif.tsv', header=TRUE, sep='\t')
# Call ComBat
ComBat(dat=dat,batch=sif$Batch, mod=NULL)

无论如何，我的输出是:

Anyway my output is:

Found 2 batches
Found 0  categorical covariate(s)
Found 54675 Missing Data Values
Standardizing Data across genes
Error in solve(t(des) %*% des) %*% t(des) %*% y1 : 
  requires numeric/complex matrix/vector arguments

数据的数据格式为:

probe set    <sample1>   ...    <sampleN>
<gene_name>  <value1>    ...    <valueN>
...

sif的数据格式为:

Data format for sif is:

Array name   Sample name   Batch
<Array1>     <Sample1>     <Batch1>
...

任何提示都值得赞赏.如有需要，我会提供更多信息.

Any hint is appreciated. I'll provide more info if needed.

谢谢

推荐答案

我已经弄清楚了如何做，并添加了:

I have figured out how to do it, adding:

# Remove NA from end of lines
l_dat = length(dat)
dat[l_dat] <- NULL
# Remove probe set from beginning of lines
dat[1] <- NULL

在ComBat调用之前.这是因为最后一列包含NA值(下一条警告消失了:

just before the ComBat call. This because last column contains NA values (next warning goes away:

Found 54675 Missing Data Values

)，第一列包含引发下一个错误的探针集(非数值):

), and first column contains probe set (non numeric values) that raise next error:

Error in solve(t(des) %*% des) %*% t(des) %*% y1 : 
  requires numeric/complex matrix/vector arguments

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