This is a test version of Biostars. For the public version, visit https://www.biostars.org.
lfcShrink function in DEseq2 is giving me an error

Hi,

lfcShrink function in DEseq2 is giving me the following error: Error in lfcShrink(dds = dds, res = res_deseq2) : res should be a DESeqResults object, for GRanges output use 'format'

My code is:

dds = DESeqDataSetFromMatrix(countData = count_data, colData = pheno_data, design = ~ genotype)
dds = DESeq(dds)

res_deseq2 = results(dds, contrast = c("genotype", "Friedreichs_ataxia","Control"), tidy = TRUE)
lfcShrink_res_deseq2 = lfcShrink(dds=dds, contrast = c("genotype", "Friedreichs_ataxia","Control"), res = res_deseq2)

My DEseq2 is 1.2.22

rna-seq
• 4,956 views • link
written by Fawzi Yassine • Fawzi Yassine

Is your version v1.2.22 or the current version (as of writing, 18th March 2019), v1.22.2?

What is the output of:

typeof(res_deseq2)
class(res_deseq2)

?

Also, please paste the output of sessionInfo()

• 0 views • link
written by Kevin Blighe Kevin Blighe

How did you solve it? Please share for the community.

• 0 views • link
written by ATpoint ATpoint

1 answer

Using results with tidy=T will coerce it to data.frame (see ?results), but lfcShrink wants GRanges as suggested in the error message. Use tidy=F or don't specify it at all as GRanges is default.

Error in lfcShrink(dds = dds, res = res_deseq2) : res should be a DESeqResults object, for GRanges output use 'format'

• 0 views • link
written by ATpoint ATpoint

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
. Upvote|Bookmark|Accept

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this
  • Explanation of DESeq factor leveling
    written by bthom • bthom
    Can someone help me to understand why the following code returns different results for df (66 DEGs) and df_1 (113 DEGs). As far as I …
  • Error function vst in DESeq2
    written by Larissa • Larissa
    ```r dds <- DESeqDataSetFromMatrix (countData = countdata, colData = metadata, design = ~ Condition + Genotype) dds <- estimateSizeFactors(dds) vst_data <- vst(dds, blind = TRUE) …
  • DESEQ2 Code
    written by ananta.kapoor • ananta.kapoor
    # Load the DESeq2 library library(DESeq2) # Read your count data counts <- read.csv("C:/Users/anant/OneDrive/Documents/RNASeq/count_data.csv", row.names = 1) # Read the metadata metadata <- read.csv("C:/Users/anant/OneDrive/Documents/RNASeq/Metadata.csv") # …
  • DESeq2 results function not working
    written by mrk • mrk
    I'm trying to use DESeq2 to do differential expression analysis. I have a simple design where there are two groups. Running the function seems to …
  • DESeq2 problem "DESeqDataSetFromMatrix function"
    written by ania.karwot • ania.karwot
    I have a problem with DESeq2 function DESeqDataSetFromMatrix: library(DESeq2) library(ggplot2) countData <- read.csv('file.csv', header = TRUE, sep = ",") head(countData) metaData <- read.csv('file_meta.csv', header = …
  • Question: can not obtain DESeq2 results
    written by zjxia • zjxia
    Dear all, I am trying to run DESeq2 to get the list of differential expressed genes between tumor and normal samples. However I could not …
  • Differential expression analysis using DESeq2
    written by prameelaawale • prameelaawale
    Hello everyone: I am new in using DEseq2. I am trying to analyze differential expression data using a publicly available data for my final project. …
  • DESeq2 log2 fold change
    written by bioinfonerd • bioinfonerd
    Hi everyone, I did the DESeq2 on my Nanostring gene expression data using the below code: dds <- DESeqDataSetFromMatrix(countData = counts_set,colData = annotation,design = ~ …
  • heatmap using DESeq2
    written by sumithrasank75 sumithrasank75
    I am trying to generate a heat map of the top differentially expressed genes between two samples. I have used DESeq2 to identify these. My …
  • How to do a heatmap (with pheatmap) when I have a multifactorial design with 3 replicates
    written by ivanasabljic • ivanasabljic
    **I load the table with the counts from HTSeq and then I ran de DESEq2 as follows:** condition = c("control","control","control","treated","treated","treated","control","control","control","treated","treated","treated") genotype = c("A","A","A","A","A","A","B","B","B","B","B","B") dds <- …