Tag: rlogTransformation

Choosing between VST and rlog for PCA for outlier identification in DESeq2 when small number of samples

I am looking at differential genes between disease cases and controls (35 sample in total). I ran DESEQ2 with the raw counts of protein coding genes from my total RNA sequencing experiment to identify my DEGs. I understand that when doing PCA, its better to transform the normalized data to…

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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 <-…

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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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