Question: Issue with finding .idat files when analysing illumina methylation microarrays using RnBeads
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gravatar for rasii
3.1 years ago by
rasii0
rasii0 wrote:

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

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