Getting erros from dds
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beslinail • 0
@d4a633b9
Last seen 8 hours ago
Turkey

After running the following code, I am getting the error. What Should I do to solve this problem? thanks

Code should be placed in three backticks as shown below

 counts <- read.delim('counts.csv', header=TRUE, row.names = 1, sep = ",") counts <- counts[which(rowSums(counts) >50),] condition <- factor(c("Ctrl1","Ctrl2","Ctrl3", "AD1","AD2","AD3"))
colData <- data.frame(row.names=colnames(counts), condition)

dds <- DESeqDataSetFromMatrix(countData = rounded_counts, colData = colData, design = ~condition)

dds <- DESeq(dds)

# please also include the results of running the following in an R session

sessionInfo( )

 estimating size factors estimating dispersions Error in checkForExperimentalReplicates(object, modelMatrix) :

The design matrix has the same number of samples and coefficients to fit, so estimation of dispersion is not possible. Treating samples as replicates was deprecated in v1.20 and no longer supported since v1.22.

DifferentialExpression DESeq2 • 96 views
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swbarnes2 ★ 1.0k
@swbarnes2-14086
Last seen 6 hours ago
San Diego

Look at the vignette. Does every sample have its own unique value in ColData in the example data in the vignette?