Reading Illumina Final Report Using Beadarraysnp R Package

Question

[venks]

Hi,

I have created a report file from my genotyping data in Genome Studio. I was trying to use the R package "beadarraySNP"

This is the error that I got

**"Error in read.SnpSetIllumina("finalreport.txt",  : 
Sample sheet error, column(s) Sample_Name, Sentrix_Position, Sample_Plate, Pool_ID, Sentrix_ID are not available"**

Infact I tried using "Nochecks=TRUE. It doesn't seem to work. Any help/suggestion is appreciated.

Thanks

[Giovanni M Dall'Olio]

can you post the first lines of the file "finalreport.txt"? Otherwise, it's difficult for us to understand what is going wrong.

Answer 1

[Matt Shirley]

Based on page 28 of the documentation, it looks like you might be specifying the final report file where you really should be specifying the sample sheet. I think you need to do something like:

SNPdata <- read.SnpSetIllumina("samplesheet.csv", reportfile="final report.txt")

Where both files reside in the current directory.

[venks]

Thanks Matt. I tried inputting the sample Sheet through a data frame. It shows the "missing column error for sample sheet". I exported the report from Genome studio. I do not know why the Sample_map file wasn't able to generate all the required columns.

[Matt Shirley]

Based on the documentation, I think you are supposed to give a string containing the file name of the sample sheet, not the actual data. You might be over-thinking this :)

[venks]

I tried the same ..

Error in read.SnpSetIllumina(samplesheet = "C:\Users\gen\Sample_Map.txt", : Cannot find "[Data]" in samplesheet file

I ended up getting this error even if I have the data in the samplesheet.I am still not sure if I ended up messing up the data or the program..

Thanks again.

Answer 2

[Jan Oosting]

When you have also saved the sample_map while saving the final report in Genome Studio you can do

SNPdata<- read.SnpSetIllumina(Sample_Map2Samplesheet("sample_map.txt"),reportfile="finalReport.txt",nochecks=TRUE)

Answer 3

[venks]

SNPdata<- read.SnpSetIllumina(Sample_Map2Samplesheet("sample_map.txt"),reportfile="finalReport.txt",nochecks=TRUE)

Blockquote

Sample_Map2Samplesheet - creates a samplesheet

Blockquote

Nochecks= TRUE when we don't have all the fields in the final report