Question: Problems with ArrayExpress datasets downloads on Bioconductor
0
gravatar for Davide Chicco
3 months ago by
Canada
Davide Chicco80 wrote:

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!

bioconductor arrayexpress • 226 views
ADD COMMENTlink modified 11 weeks ago by h.moosavi570 • written 3 months ago by Davide Chicco80
0
gravatar for jorgeklz
3 months ago by
jorgeklz0
Chile
jorgeklz0 wrote:

Hi. I got the same error. Did you solve it?

ADD COMMENTlink written 3 months ago by jorgeklz0
0
gravatar for h.moosavi57
11 weeks ago by
h.moosavi570 wrote:

same problem. Would appreciate if someone could give a solution . Thanks in advance.

ADD COMMENTlink written 11 weeks ago by h.moosavi570
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