This is a test version of Biostars. For the public version, visit https://www.biostars.org.
just trying to launching my DE-seq2 by csv but isn't work...

hello sir, im korean and currently work in dpt, bioenginearing... first of all, my major is basically experiment and im suddenly transferred into Industry-University Cooperation Foundation. its my first time coding r script. so i have to run DE-seq2 so that make my MA-plot(and have no idea any of r script knowledgement) ive tried so many time of this link : https://lashlock.github.io/compbio/R_presentation.html

and my code is right here;

library( "DESeq2" )
library(ggplot2)

countsName <- "http://bioconnector.org/workshops/data/airway_scaledcounts.csv"
download.file(countsName, destfile = "airway_scaledcounts.csv", method = "auto")

countData <- read.csv('airway_scaledcounts.csv', header = TRUE, sep = ",")
head(countData)

metaDataName <- "http://bioconnector.org/workshops/data/airway_metadata.csv"
download.file(metaDataName, destfile = "airway_metadata.csv", method = "auto")

metaData <- read.csv('airway_metadata.csv', header = TRUE, sep = ",")
metaData

dds <- DESeqDataSetFromMatrix(countData=countData, 
                              colData=metaData, 
                              design=~dex)
dds <- DESeq(dds)

?DESeq

res <- results(dds)
head(results(dds, tidy=TRUE)) #let's look at the results table

and error code emerged, but do not know what's going wrong...

Error in DESeqDataSetFromMatrix(countData = countData, colData = metaData,  : 
  ncol(countData) == nrow(colData) is not TRUE

in korea server, i cannot find how to fix this error code and i wrote this one with my lack of english skill. please help me (ㅠㅁㅠ)

de-seq2 r de-seq2
• 2,377 views • link
written by Lily • Lily

I think this tutorial is deprecated as the files do not exist anymore

• 0 views • link
written by Basti • Basti

Number of samples in the data and metadata is not matching.

• 0 views • link
written by cpad0112 cpad0112

thank you so much...! have to find any other code to run TAT

• 0 views • link
written by Lily • Lily

1 answer

The error means that the order or the row of the metadata and the columns in your counts are not matching. DESEq2 expect the order to be the same as it doesn't do the checking and reordering for you. Order the two tables so that row 1 of the metadata table is the same as the column 1 in the count matrix, and so on.

Have a look at the current DESEq2 documentation section Count matrix input.

• 0 views • link
written by fracarb8 fracarb8

thannk you so so much!! appreciate it!! seems better to try fixing that dds code! thank you!

• 0 views • link
written by Lily • Lily

Log in to answer this question.

More posts like this