Hello! I come across one article（Transcriptome analysis of non human primate-induced pluripotent stem cell-derived cardiomyocytes in 2D monolayer culture vs. 3D engineered heart tissue）, and I would like to use the expression matrix associated with the GSE156237 dataset. However, I noticed that the author have uploaded a VSD matrix processed with VST to the GEO website. Is there any other ways to do differential analysis on vsd data, if I do not want to from the raw fastq.
Thank you very much for your time and consideration.
hi thanks a lot. It is a matrix, not much related to GEO, more related to DESEQ2, I want to know if raw count after VST function , then can use wilcox or limma to do gene differential analysis
I do not understand what you mean. Please search previous posts. vst can be used with limma, and DESeq2 needs raw counts as described in the vignette.
GSE156237_DESeq2_vsd_exp.txt.gz I have a gene expression matrix, the data in it was transformed by vst, how can I do differential analysis on this data
thanks a lot