Hi all
I need to download 3 datasets from ArrayExpress: E-MTAB-5273, E-MTAB-5274, and E-MTAB-4451. I tried to do that in R by using the ArrayExpress() function of the ArrayExpress package on Bioconductor, but it generate errors for all the three cases. I am using R version 3.5.2 on Linux Ubuntu 18.
Here are the command I used and the errors generated.
First dataset -- E-MTAB-5273
I tried to download the first dataset through the following R commands:
# library installation and loading if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager") BiocManager::install("ArrayExpress", version = "3.8")
library("ArrayExpress")
rawset = ArrayExpress("E-MTAB-5273") # download
and here's the error
And it generated the following error:
Unpacking data files
ArrayExpress: Reading pheno data from SDRF
Error in `.rowNamesDF<-`(x, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique value when setting 'row.names':
‘Burnham_sepsis_discovery_raw_237.txt’
Second dataset -- E-MTAB-5274
I tried to download the second dataset through the following R command:
rawset = ArrayExpress("E-MTAB-5274")
and it generated the following error:
Unpacking data files
ArrayExpress: Reading pheno data from SDRF
Error in `.rowNamesDF<-`(x, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique value when setting 'row.names':
‘Burnham_sepsis_validation_raw_108.txt’
Third dataset -- E-MTAB-4451
I tried to download the third dataset through the following R command:
rawset = ArrayExpress("E-MTAB-4451")
And I get the error:
Unpacking data files
ArrayExpress: Reading pheno data from SDRF
Error in which(sapply(seq_len(nrow(pData(ph))), function(i) all(pData(ph)[i, :
argument to 'which' is not logical
In addition: Warning message:
In readPhenoData(sdrf, path) :
ArrayExpress: Cannot find 'Array Data File' column in SDRF. Object
might not be created correctly.
Questions: why am I getting these errors?
How to overcome these errors?
My goal is to be able to read the file content and the raw data.
Thanks!
