![]() So let’s say I have a matrix expressionMatrix that represents gene expression, with genes as rows and samples as columns, but after it has undergone some transformations. Vsd <- varianceStabilizingTransformation(dds, blind = FALSE) ![]() I’ve chosen design = ~Treatment because I’m interested in seeing the effect of inducing the shRNA by DOX dds <- DESeqDataSetFromMatrix(countData = countsData, colData = metaData, design = ~ Treatment) Once the data is imported into R, we can tell our friendly DESeq package to convert it into a more versatile format. # Sample Treatment Hairpin Cell_Line Color Subtype Sample_name This metaData looks like this tibble::as_data_frame(metaData) For instance, whether the cells were treated with DOX or not, etc. The other one contains meta data about the experiment. I named it countsData and it looks like this: tibble::as_data_frame(countsData) One of them has genes as rows and samples as columns. I may write a post another day on how alignment works and how to imported the aligned counts, but for now that’s already been done.
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