IDAT Files not present

[nellieca...@gmail.com]

Hello

can I please get help on this. 

I keep getting errors with regards to my IDAT files 

Error in logger.error(txt) : 

  Some IDAT files are not present in the supplied base directory, for instance 1.00973e+11_R01C01_Red.idat, 1.00973e+11_R01C01_Grn.idat, 1.00973e+11_R03C02_Red.idat, 1.00973e+11_R03C02_Grn.idat, 1.00973e+11_R05C01_Red.idat, 1.00973e+11_R05C01_Grn.idat

Nellie 

[Victor Yuan]

It looks like your filenames have been converted to scientific notation (e.g. 1007723000_Red.idat -> 1.0077e+11_Red.idat).

This usually happens when you open and save .csv files with Excel. Check your filenames are correct and then try loading in the idats again.

Victor

[nellieca...@gmail.com]

Is there a way to prevent my csv file from being formatted to SCI notation 

[Indranil Sinha]

Open the original file in excel. select your data, right click, and click "Format cells..." and choose Number (with decimal places: 0). Save as .csv and open the file again in some text editor. If you open the .csv file in excel the long numbers will be converted into SCI notation by default. 

[nellieca...@gmail.com]

still experiencing the same error code. formatting the cells and opening it on text doesnt really do much.

is it possible that something is wrong with my codes 

# load the package

library(RnBeads)

# define the directory structure

data.dir <- "/Users/Nelly/Desktop/research/Ohm_Project_007_Data_Package/idat"

idat.dir <- file.path(data.dir, "idatt")

sample.annotation <- file.path(data.dir, "sample.annotation.csv")

###Directory where the output should be written to

analysis.dir <- "/Users/Nelly/Desktop/research/Ohm_Project_007_Data_Package/analysis"

#Directory where the report files should be written to

report.dir <- file.path(analysis.dir, "reports_details")

data.source <- c(idat.dir, sample.annotation)

rnb.options(filtering.sex.chromosomes.removal=TRUE, identifiers.column="Sample_Name")

rnb.run.analysis(dir.reports=report.dir, sample.sheet=sample.annotation,data.dir=idat.dir, data.type="infinium.idat.dir")

file.exists(report.dir)

[Indranil Sinha]

Hi,

From your code it looks like your data dir is: "../Ohm_Project_007_Data_Package/idat" and all idat files are in "../Ohm_Project_007_Data_Package/idat/idatt"

Please check if this is true.

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Best Regards,

Indranil.