Issue in import files in Metaboanalyst
0
0
Entering edit mode
22 months ago
Andrea ▴ 10

Hi,

I'm trying to use metaboanalyst package, but I'm encountering a problem in the data file loading. I have a csv file with samples in rows and predictors in column. When I use the Read.TextData I get the Error: $ operator is invalid for atomic vectors. How can I solve the issue? Thank you

mSet<-InitDataObjects("conc", "roc", FALSE)
"load data file (samples in rows, predictors in columns, second column = disease phenotype)"
mSet<-Read.TextData(mSet, File.csv, "rowu", "disc")
Error: $ operator is invalid for atomic vectors
Metaboanalyst R • 1.3k views
ADD COMMENT
0
Entering edit mode

It is related to your .csv file, however we do not know what does it look like. Check that this file is correctly formatted by comparing it with test datasets : https://www.metaboanalyst.ca/docs/Format.xhtml

ADD REPLY
0
Entering edit mode

Thank you. I've check it and it seems correctly formatted. I've also created a very small csv table from scratch just to check, but I've got the same problem. Could it be due to some dependencies?

I'll also try with one of the file downloaded from the site.

Thank you

ADD REPLY
0
Entering edit mode

If you can share your small .csv table example, we would be happy to help you

ADD REPLY
0
Entering edit mode

Here the link to the file: https://www.dropbox.com/s/w1t954eaxqej6i1/Prova_metab.csv?dl=0

I've also tried with a file downloaded from the Metaboanalyst file, but I had the same error

ADD REPLY
0
Entering edit mode

I have no error after downloading your file and running your code, maybe you need to update your package ?

ADD REPLY
0
Entering edit mode

Yeah, I think so, but I don't know what I must update. I've installed R and the package on a new ubuntu machine two weeks ago. Thank you for the help

ADD REPLY

Login before adding your answer.

Traffic: 1751 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6