Issue with finding .idat files when analysing illumina methylation microarrays using RnBeads
0
0
Entering edit mode
rasii • 0
@rasii-10044
Last seen 8.2 years ago

Hi,

 

I'm trying to analyse my Illumina methylation EPIC microarray data using RnBeads and I get the following error when i do:

 

rnb.run.analysis(dir.reports=reportDir, sample.sheet=sampleSheet, data.dir=idatDir, data.type="infinium.idat.dir")

2016-08-28 09:37:17     0.5  STATUS                                                                                                                                                             STARTED RnBeads Pipeline

2016-08-28 09:37:17     0.5    INFO                                                                                                                                                                 Initialized report index and saved to index.html

2016-08-28 09:37:17     0.5  STATUS                                                                                                                                                                 STARTED Loading Data

2016-08-28 09:37:17     0.5    INFO                                                                                                                                                                     Number of cores: 1

2016-08-28 09:37:18     0.5    INFO                                                                                                                                                                     Loading data of type "infinium.idat.dir"

2016-08-28 09:37:18     0.5  STATUS                                                                                                                                                                     STARTED Loading Data from IDAT Files

2016-08-28 09:37:18     0.5   ERROR                                                                                                                                                                         Some IDAT files are not present in the supplied base directory, for instance 200357150012_Red.idat, 200357150012_Grn.idat, 200357150012_Red.idat, 200357150012_Grn.idat, 200357150012_Red.idat, 200357150012_Grn.idat

Error in logger.error(txt) : 

  Some IDAT files are not present in the supplied base directory, for instance 200357150012_Red.idat, 200357150012_Grn.idat, 200357150012_Red.idat, 200357150012_Grn.idat, 200357150012_Red.idat, 200357150012_Grn.idat

 

I have rechecked my folder that holds the .idat files and I have all the necessary files in there so I'm not sure why its giving me this error.

 

Any help is highly appreciated.

 

Thanks,

Rasi

rnbeads methylation illumina epic microarray • 1.7k views
ADD COMMENT

Login before adding your answer.

Traffic: 551 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