Tag: logCPM

Gene Expression Analysis Steps ?

Hi everybody, I’m new in this field. I’m trying to replicate a paper to train my self . The results come out pretty the same but not exactly the same, so I wanted to know if all my steps are right or if I’m missing something ( or even completely…

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use gene symbol in heatmap instead of ensemble geneID

Hi All I plot the heat map for my logCPM successfully but using Ensemble geneIDs. I need the heatmap to have the gene symbols, I can convert the ensemble gene IDs to gene IDs fine, but don’t know how to reflect this on the heatmap. My code for the heatmap…

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Is there a way to mark up specific genes in MA-plot?

Is there a way to mark up specific genes in MA-plot? 1 Dear, everyone, I have this table, and created MAplot using the following steps. In this plot, I would like to mark up only the genes that I specify:for example, I would like to display the gene name in…

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Use Spike-Ins or TMM-normalization

Use Spike-Ins or TMM-normalization 1 Hi all, Sorry for all my questions lately, but as a novice which has to figure out how to analyse QuantSeq data, this forum has been a great and indispensible help for me. I’m doing a human transcriptomics analysis where we have QuantSeq data for…

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Calculate fold change in edgeR with one sample per condition

Hi, We have run a pilot RNA-Seq study with one sample per condition, this is just a test run. I understand there is no valid statistical test in this case, however just curious to obtain differential expression through edgeR package in R assuming dispersion = 0.4 for the human data….

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How to convert log2 scale RNA-Seq expression data to linear scale data

How to convert log2 scale RNA-Seq expression data to linear scale data 0 Hi, We have run a pilot RNA-Seq study and I used edgeR package to obtain differential expression results. The results output a gene column along with the logCPM, logFC and p-value column. I have a question regarding…

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