I want to use the satuRn package to test for differential transcript usage between two diets. My data is in the sumExp. I set up the contrast matrix L and try to run the satuRn::testDTU function as described in the vignette. I keep on running into the same error and dont unterstand fully where it comes from. Does someone have experience with that can can help?

I’m working on a project that involves performing GSVA using the GSVA package in R. Specifically, I’m trying to use the single-sample Gene Set Enrichment Analysis (ssGSEA) method. However, I’m encountering persistent errors related to the new API introduced in the Bioconductor release 3.18. The function signatures and usage have changed, and I’m having trouble adapting my code to the new requirements.

I’m working on a project that involves performing GSVA using the GSVA package in R. Specifically, I’m trying to use the single-sample Gene Set Enrichment Analysis (ssGSEA) method. However, I’m encountering persistent errors related to the new API introduced in the Bioconductor release 3.18. The function signatures and usage have changed, and I’m having trouble adapting my code to the new requirements.

I’m trying to plot fcs (flow cytometry) file in r by flowCore package, but I don’t know if my problem is with the package or the coding. I’ll explain what I did and I’m hoping you guys can help me out here.

Is it possible to do this in the same line of code, using the dotplot function from clusterProfiler. I’ve been looking for information I got this line

I am currently taking a datacamp course on the bioconductor package. There’s a section where you use the zika genome using the BioStrings package. I’m wondering where I could load this variable? The course says the genome was downloaded from https://www.ncbi.nlm.nih.gov/nuccore/NC_012532.1. Inside of datacamp if I do dput(zikaVirus) (the variable in the session is zikaVirus I get

I was trying to use NanoTube and NanoStringDiff packages to normalize my NanoString RNA seq data. We incorporate the panel standards to address the batch effect but I don’t know how to use these two packages to normalize the data incorporating the panel standards. Alternatively, if I use nSolver (NanoString designed GUI software) to normalize the data, can I use packages such as limma or DESeq2 to perform differential expression on the normalized count matrix?