https://divingintogeneticsandgenomics.com/tags/microarray/ Recent content in Microarray on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Thu, 19 Dec 2013 19:49:00 -0800 https://divingintogeneticsandgenomics.com/archive/log2-fold-gene-expression-change-heatmap/ Thu, 19 Dec 2013 19:49:00 -0800 https://divingintogeneticsandgenomics.com/archive/log2-fold-gene-expression-change-heatmap/ I was looking at two different microarray data sets. In each experiment, the authors knocked down a transcription factor (TF) and examined the gene expression change respectively. I wanted to know whether there are any co-upregulated or co-downregulated genes after knocking down the TFs. I analyzed the microarray data by bioconductor. See one of the examples I blogged before GEOquery to access GEO datasets Because those are two different experiments done in different platforms and in different labs, I can not put the raw expression data together. https://divingintogeneticsandgenomics.com/archive/geoquery-to-access-geo-datasets/ Sat, 07 Dec 2013 22:08:00 -0800 https://divingintogeneticsandgenomics.com/archive/geoquery-to-access-geo-datasets/ I was reading a paper Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells , and wanted to re-analyze the microarray data. In the paper, Hao wu et.al. knocked down Tet1, a protein can convert 5-methylcytosine to 5-hydroxymethlycytosine, and looked at gene expression change in mouse ES cells. It was my first time to look at mouse microarray data set, but I was aware of that GEOquery, a bioconductor package, can do the job very easily.