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Entering edit mode
9.9 years ago
venks ▴ 730

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

r illumina bioconductor genotyping snp • 4.1k views
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Entering edit mode

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

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Entering edit mode
9.9 years ago

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.

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Entering edit mode

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.

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Entering edit mode

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 :)

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Entering edit mode

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.

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Entering edit mode
9.9 years ago
Jan Oosting ▴ 920

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)

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Entering edit mode
9.9 years ago
venks ▴ 730

Blockquote

Sample_Map2Samplesheet - creates a samplesheet

Blockquote

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