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ziyili20 / TOAST

Tools for the analysis of heterogeneous tissues
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Is it possible to use TOAST for microarray data? #8

Open sam-israel opened 3 years ago

sam-israel commented 3 years ago

Is it possible to use TOAST for microarray data? Are there modifications or specifications that should be used when analyzing microarrays?

sam-israel commented 3 years ago

Actually, I see that it is definitely possible.

This package is devoted to analyzing high-throughput data (e.g. gene expression microarray, DNA methylation microarray, RNA-seq) from complex tissues.

My apologies. I understand that the microarray data should not be in log space?

In the vignette, it is not in log space

CBS_mix[1:4,1:4]

##       X17.002 X17.006 X17.019 X17.023
## ABCB4    96.0  107.50  110.00    92.3
## ABCB9    98.3  109.75  103.85    92.1
## ACAP1   196.8  217.80  351.00   140.7
## ACHE     92.7   97.20   87.10    87.1
sam-israel commented 3 years ago

I have found the answer for it in the article

https://doi.org/10.1093/bioinformatics/btz196

Theoretically, mixing takes place at the raw scale and linear deconvolution is expected to work on the same scale. However, real biological data from high-throughput technology are complex and often include many sources of noise, distortion and anomaly that cannot be fully captured by simple parametric simulation. ... As a result, real data applications may find that analyzing the log-scale data delivers similar or even better performance