Tag: logCPM

how to test for differential expression in samples where a global increase in gene expression is expected

As the title suggestions, I’m wondering what the best way to test each gene in a count matrix containing two groups is, where one group is expected to have a global increase in gene expression. I need to use spike-in normalized RPKM data, so from my understanding of DESeq, it…

Continue Reading how to test for differential expression in samples where a global increase in gene expression is expected

Why we are using filtering >0 for up and

Why we are using filtering >0 for up and <0 for down after TopTags() to extract de genes ids? 0 How to extract list of DE genes after EdgeR? With summary() I get number of Up and Down expressed genes. And I would like to extract the gene IDs for…

Continue Reading Why we are using filtering >0 for up and

Associating between results obtained after running Trinity’s run_DE_analysis.pl and genes

Associating between results obtained after running Trinity’s run_DE_analysis.pl and genes 0 Hi.How can one associate between the generic transcript names and the actual genes of the studied organism? Here are the first few lines of the output file kallisto.gene.counts.matrix.Control_vs_Serum.edgeR.DE_results (which I understood is the relevant one for differential expression analysis):…

Continue Reading Associating between results obtained after running Trinity’s run_DE_analysis.pl and genes

Mapping interindividual dynamics of innate immune response at single-cell resolution

Ethical compliance This project was approved by the Wellcome Sanger Institute Animal Welfare and Ethical Review Body and complied with all relevant ethical regulations regarding animal research and human studies. Human cells were obtained from HipSci24, where they were collected from volunteers recruited from the National Institute for Health and…

Continue Reading Mapping interindividual dynamics of innate immune response at single-cell resolution

Limma returned only positive logFC values

Limma returned only positive logFC values 0 I want to obtain the upregulated and downregulated genes using limma. However, all the DEGs returned by my code have positive LogFC and none are downregulated (negative LogFC). This observation is consistent across multiple distinct dataframes. Is there something wrong with my code?…

Continue Reading Limma returned only positive logFC values

Circulating miRNA expression in long-standing type 1 diabetes mellitus

Participants This is an observational case–control study, carried out in adult patients who attended the Endocrinology and Nutrition Service of the Central University Hospital of Asturias, between June 2019 and December 2021. Written informed consent was obtained from all participants and the study was conducted in accordance with the principles…

Continue Reading Circulating miRNA expression in long-standing type 1 diabetes mellitus

Transcriptomic analysis of benznidazole-resistant and susceptible Trypanosoma cruzi populations | Parasites & Vectors

Overview of sample sequencing We compared the transcriptomes of BZ-resistant (17LER) and wild-type (17WTS) T. cruzi populations. cDNA libraries were constructed, sequenced and analysed for identifying the DE transcripts associated with resistance to BZ. The following parameters were evaluated using the read-quality analysis: (i) quantity of the sequenced reads; (ii)…

Continue Reading Transcriptomic analysis of benznidazole-resistant and susceptible Trypanosoma cruzi populations | Parasites & Vectors

CI for logCPM (fitted values)

CI for logCPM (fitted values) 1 @hakusen03-10599 Last seen 10 hours ago United States Hello, I’m plotting fitted curves for my genes of interest using logCPM, and I need to include the CI. I’m not sure how to do this using using the edgeR DEGlist. Do you have a recommendation…

Continue Reading CI for logCPM (fitted values)

Obtention of the binomial transformed count table with edgeR

Hello! When performing differential expression analysis with RNA-Seq data using DeSeq2, and after data normalisation, there is the option to extract a count table with the transformed abundance levels using the variance stabilisation transformation (vst) method. Line of code vst counts extraction: vst_dds <- vst(res) The DeSeq2 manual itself indicates…

Continue Reading Obtention of the binomial transformed count table with edgeR

manually calculate log2 fold change and compare

Hi everybody, I am struggling trying to calculate log2FC manually with an RNA-seq experiment that has no replicates. I know this question has been posted but hadn’t been able to transfer the answers to my data. So I have 3 conditions, let’s say HpA, SpA and Empty. I would like…

Continue Reading manually calculate log2 fold change and compare

Is there anyway to cancel CPM normalization?

Is there anyway to cancel CPM normalization? 1 I am performing a meta-analysis and I am looking for processed RNA-seq data. I would prefer counts data, but if that is not available, then TPM normalized data would be acceptable. I found a dataset that only has logCPM normalized RNA-seq data…

Continue Reading Is there anyway to cancel CPM normalization?

Secondary Filtering of DE Results to Eliminate Lowly-Expressed Transcripts

Hello, I’m currently trying to analyze an RNA-seq data set of about 10500 samples (including biological replicates) and initially noticed some strange outputs in my differential expression output file. I am using the CIRIquant pipeline with the built-in differential expression function which uses the edgeR module to calculate DE circular…

Continue Reading Secondary Filtering of DE Results to Eliminate Lowly-Expressed Transcripts

Normalizing expression values

Normalizing expression values 0 Hello everyone! I am starting out with scRNA-seq preprocessing and quality control analysis through Scanpy. I have found a tutorial and 2 of the steps are not completely clear for me and I would like to ask if anyone could help me out. The first step…

Continue Reading Normalizing expression values

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…

Continue Reading Gene Expression Analysis Steps ?

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…

Continue Reading use gene symbol in heatmap instead of ensemble geneID

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…

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

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…

Continue Reading Use Spike-Ins or TMM-normalization

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….

Continue Reading Calculate fold change in edgeR with one sample per condition

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…

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