Tag: rlogTransformation

Correct way to make multiple comparisons on DESeq2?

I have a project where I have done RNA-seq (paired-end sequencing on Illumina HiSeq) of a worm at different days of development i.e. Ages 0-12. For each age, I have sequenced 3 replicate specimens. I’m new to DESeq2 and I was wondering if what I did below is correct. library(DESeq2)…

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r – How to replace row names in DESeq2 rlogTransformation matrix with actual gene name info present on another sheet?

I’m new to R and DESeq2 and I’m trying to run differential expression as below library(DESeq2) count_file_names <- grep(“counts”,list.files(“HTSeq_counts”),value=T) host_type < c(“Damaged”,”Control”) sample_information <-data.frame(sampleName = count_file_names, fileName = count_file_names, condition = host_type) DESeq_data <- DESeqDataSetFromHTSeqCount(sampleTable = sample_information, directory = “HTSeq_counts”, design = ~condition) colData(DESeq_data)$condition <- factor(colData(DESeq_data)$condition,levels = c(‘Damaged’,’Control’)) rld <-…

Continue Reading r – How to replace row names in DESeq2 rlogTransformation matrix with actual gene name info present on another sheet?

How to replace row names in DESeq2 rlogTransformation matrix with actual gene name info present on another sheet?

I’m new to R and DESeq2 and I’m trying to run differential expression as below library(DESeq2) count_file_names <- grep(“counts”,list.files(“HTSeq_counts”),value=T) host_type < c(“Damaged”,”Control”) sample_information <-data.frame(sampleName = count_file_names, fileName = count_file_names, condition = host_type) DESeq_data <- DESeqDataSetFromHTSeqCount(sampleTable = sample_information, directory = “HTSeq_counts”, design = ~condition) colData(DESeq_data)$condition <- factor(colData(DESeq_data)$condition,levels = c(‘Damaged’,’Control’)) rld <-…

Continue Reading How to replace row names in DESeq2 rlogTransformation matrix with actual gene name info present on another sheet?

Can I remove the control in differential expression analysis?

Hi there, Essentially, my experimental design is control vs treatment. Cells were sorted based on fluorescence, so there are 4 different “colors” of treated cells, i.e. red, green, green+red, and blue+green+red. I am interested in how the colors differ from one another. And, I have duplicates for all colors and…

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same padj for all the genes after DEseq analysis

Hi everyone, I have done a pair comparison with DEseq2 to find differentially expressed genes between two samples with 6 replicates, for the DEseq2 result, i got exactly same padj value for all the genes and it is not significant, is this normal ? I don’t think the padj should…

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