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jaleesr / TrendCatcher

TrendCatcher is an open source R-package that allows users to systematically analyze and visualize time course data. Please cite "Temporal transcriptomic analysis using TrendCatcher identifies early and persistent neutrophil activation in severe COVID-19" by Xinge Wang et al published in JCI Insight (2022) - https://insight.jci.org/articles/view/157255
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Raw or normalized microarray data for the analysis #3

Closed bugie19 closed 2 years ago

bugie19 commented 2 years ago

Hi,

your tool is really outstanding. thanks for your handworks.

Can we use raw or normalized microarray data instead of bulk RNAseq for the analysis? I really appreciate your response.

best regards,

Bugie

wangxinge commented 2 years ago

Dear bugie19, Thank you for liking TrendCatcher. The tool is tailored to analyze RNA-seq count data, for which we adapted the negative binomial distribution. Also, all the simulation datasets used to evaluated the model performance were performed on RNA-seq count data. The microarray data follows a different distribution, I don't think it is ideal to run it with TrendCatcher.