What is present and absent calling in high-throughput data?

Question

[mirzaei86.vahid]

Hi

I have an expression dataset, It has a column entitled absent/present calling (values 0 or 1), I have two questions:

1- Should I treat different on expression columns based on 0 or 1 ?

2- Is this column just used for Microarray or it could be used for RNA-SEQ too?

Thanks.

Answer 1

[nazaninhoseinkhan]

Can you send a few lines of your data set? I guess "absent/present calling" correspond to certain variants (SNP).

[mastal511]

If it is an expression dataset, and not a SNP array, it could indicate whether the signal was above a certain minimum threshold, perhaps after adjusting for background. This would only be used for microarrays, where each call refers to a specific location on the chip.

[mirzaei86.vahid]

thanks @mastal511, it is expression data. and from 1700 have 0 value from 33K gene ids. So I should cut 0 value?

[mirzaei86.vahid]

dear Nazanin, my data is expression profile.