Reading ilumina data in R

Question

[m.shahdoost]

Hi everybody. I have an illummina data set and I want to read them in R and make a data frame. I applied the "methylumi" package but I got the below error: Error: file 3998532076_A_Grn_Red.idat is missing for sample 3998532076_A_Grn Error: file 3998532076_A_Grn_Grn.idat is missing for sample 3998532076_A_Grn Error: all(files.present) is not TRUE

Please help me.

[andrew.j.skelton73]

The error seems quite informative - It's saying that respective files are not present. Try checking your command for reading in the IDAT files, and check the paths are correct.

[WouterDeCoster]

I have an illummina data

This can mean almost anything. Reads, bam files, raw images, variants, RNA-seq, genome sequencing, snp-array,...
Please try to be as informative as possible when asking questions.

[m.shahdoost]

Actually, I have iScan Row data including some idat files such as 3998532076_A_Grn , images and .xml files. I am not familiar with illumina data. the error says we need files like 3998532076_A_Grn.Red.idat but there is similar files with extension xml in the data set not .idat file.

[andrew.j.skelton73]

Assuming you have Illumina Methylation data, you need the idat files from the iScan, that's the typical raw data that most pipelines will use for methylation analysis.

[m.shahdoost]

Thank you for your attention. I am need to read the gene expression and change them to text files. Is there any way?

[WouterDeCoster]

Please be more specific, we are very bad at reading your mind to find out what you have and what you need.