Hi Biostar, I try to make plot as the fgsea tutorial using the same code: stats <- with(results, setNames(logFC, row.names(results))) fgseaRes <- fgsea(pathways = c2_list, …

Hi Biostar, I try to perform Differential expression at pathway level: disease_es <- gsva(disease_Par) Error in validObject(.Object) : invalid class “ExpressionSet” object: sampleNames differ between …

Hi Biostar, I would like to do differential expression at pathway level by following this tutorial. I have microarray data. Would you please tell me …

Hi all, I am try to work with normalization count data using DEseq2. I am trying their [tutorial][1], until the normalization part. `dds <- estimateSizeFactors(dds)` …

I know the [Bioconductor vignettes for GSVA][1] has a decent description of the methodological differences between the algorithms. However, I am still confused with the …

Hi, I'm analyzing RNA-seq data and i followed DESeq2 tutorial (http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-un-normalized-counts) starting from the raw counts for gene expression, I want now to perform GSVA …

SBGNview is similar and complementary to the widely used Pathview package, supporting multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP etc), with …

I am new to analysis of microarray data using R. I am using EventPointer package to analyze HTA 2.0 array data. Can someone elaborate on …

Hi, I am attempting to make some heat maps with some RNA-Seq data. I used Salmon for my quantification and followed [this][1] link to import …

I'm using trying to use [this tutorial][1] to map certain protein positions to genomic positions. The whole tutorial is focused on using the `Proteins` class …