Tag: raw_counts

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 ▴ 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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