I have normalized count matrix which is normalized using conditional quantile normalization and having negative value, I understand that these are normalized logFC values. When I am directly using into limma with following command. It is showing error. The steps:
data <- read.csv("new_count_arranged.csv", sep = ';') meta_data <- read.csv("new_pheno_sorted_comma.csv", sep = ';') y <- normalizeBetweenArrays(data)
Error in normalizeBetweenArrays(dbgap_data) : 'object' is a data.frame and not all columns are numeric
Kindly help to caluculate pvalue , padjusted value, TPM
File Format:
geneid sample1 sample2 AB1 3.09852052 9.07170501 CBF 5.30616784 -0.06336533
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You must convert
datato a numeric matrix as indicated by the errorCan you guide me about me, because when I converted it then it showed, not all columns are integers. I request for help to perform this. I am using limma first time.
I think a quick search on Google "convert dataframe to numeric r" or alternatives would give you an answer