Tag: raw_counts

A query about selecting the coefficient in glmLRT to test for by index

A query about selecting the coefficient in glmLRT to test for by index 1 @0b4d0d5b Last seen 9 hours ago Norway I am using the below set of equations for my differential expression analysis. In the glmLRT line, I was previously specifying the coef by index and since I am…

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how to determine n_cells_by_count

Hello, I followed this toturial (github.com/mousepixels/sanbomics_scripts/blob/main/single_cell_analysis_complete_class.ipynb ) in order to preceed single cell rna seq analysis using scanpy. for the first step data filtring I applied this script def pp(csv_path): adata = sc.read_csv(csv_path).T sc.pp.highly_variable_genes(adata, n_top_genes = 2000, subset = True, flavor=”seurat_v3″) scvi.model.SCVI.setup_anndata(adata) vae = scvi.model.SCVI(adata) vae.train() solo = scvi.external.SOLO.from_scvi_model(vae) solo.train()…

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Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap

Sample preparation Arabidopsis thaliana accession Col-0 seeds (hereafter Arabidopsis) were sown on square plates containing Linsmaier and Skoog medium (Caisson Labs, catalogue no. LSP03) with 0.8% sucrose solidified with 1% agar (Caisson Labs, catalogue no. A038). Plates were kept vertically for 5 days in a growth chamber under an 8:16 h light/dark…

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r – Plotting infercnv results

I’m working with matched single cell data, where we have treated and untreated samples for the same patient. I ran CNV analysis using the infercnv package. I’ve followed the tutorial: # data matrix counts_matrix <- scData@assays$RNA@counts meta = data.frame(labels = Idents(scData), row.names = names(Idents(scData))) unique(meta$labels) # check the cell labels…

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normalization – DESeq2 throwing error while normalizing raw microarray expression data due to presence of negative values

This question was also asked on Biostars I am trying to download and analyze a miRNA expression dataset from NCBI GEO (GSE25631). I specifically want non-normalized data to perform normalization and my own set of other analyses later on. Accordingly, I downloaded the Series Matrix File (to match the Sample…

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DESeq2 throwing error while normalizing raw microarray expression data due to presence of negative values

I am trying to download and analyze a miRNA expression dataset from NCBI GEO (GSE25631). I specifically want non-normalized data to perform normalization and my own set of other analyses later on. Accordingly, I downloaded the Series Matrix File (to match the Sample IDs with their phenotype) and the non-normalized…

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Embedding a known metadata onto a seurat object created using a raw_counts_mat.rdata file

Embedding a known metadata onto a seurat object created using a raw_counts_mat.rdata file 0 Hi, I am struggling to understand how to create a seurat object using a raw_counts_mat.rdata file, which you can find it here. I loaded it using the load function and created a counts dataframe, following this,…

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Build killed with signal TERM after 150 minutes of inactivity

Source: pigx-rnaseq Version: 0.1.0-1.1 Severity: serious Justification: FTBFS Tags: bookworm sid ftbfs User: lu…@debian.org Usertags: ftbfs-20230113 ftbfs-bookworm Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > input: > /<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, > /<<PKGBUILDDIR>>/tests/output/colData.tsv > output: > /<<PKGBUILDDIR>>/tests/output/report/hisat2/analysis1.deseq.report.html > log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/analysis1.report.log >…

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Merge multiple text files to create a combined dataframe and rename columns in R – General

Hi, I have multiple .txt files (each file contains 4 columns; an identifier Gene column, a raw_counts and other columns). I would like to merge those files into a combined dataframe using the common gene column. I was able to import multiple .txt files together, merge based on identifier column,…

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rna seq – R – [DESeq2] – How use TMM normalized counts (from EdgeR) in inputs for DESeq2?

I have several RNAseq samples, from different experimental conditions. After sequencing, and alignment to reference genome, I merged the raw counts to get a dataframe that looks like this: > df_merge T0 DJ21 DJ24 DJ29 DJ32 Rec2 Rec6 Rec9 G10 421 200 350 288 284 198 314 165 G1000 17208…

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DESeq2 input from GDAC firehose

Hi guys, I hope you are fine. I’m not good in English so if you couldn’t understand my question, please feel free to reply. I’m a beginner of bioinformatics. I want to practice differential expressed gene (DEG) analysis in R. The RNA seq data I used was downloaded from broad…

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Differential Gene Expression

Can you analyze in GEO2R? => No, because this is RNA-seq and not microarrays. You are lucky thought that the authors seem to provide raw counts so you can easily fede them into DESeq2. Here is a code suggestion, for details please read the DESeq2 vignette extensively, it contains answers…

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Biostar Raw_counts

Showing : raw_counts • reset 2 results • Page 1 of 1 Recent … Replies Comment: makeContrasts question by HS &utrif; 10 Hi Gordon, I’m having a hard time understanding why I’m getting few significantly expressed genes after testing for the interaction in thi… Answer: catchSalmon by Gordon Smyth 43k…

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