I am executing the deseq2 for two conditions sick and healthy. Each condition has 4 cell types defined as group (a1, b1, c1 and d1, a2, b2, c2, d2). each group has 3 replicates. (a1:3...d2:3). condition_group is third column (sick_a1, sick_a2...so ) I want to compare different contrasts like
Sample Condition Group 11 healthy a2 13 sick b1 14 sick c1 15 sick d1 17 sick a1 19 healthy b2 1 sick b1 20 healthy c2 21 healthy d2 32 healthy c2 23 healthy a2 33 healthy d2 25 sick b1 35 healthy a2 26 sick c1 3 sick d1 27 sick d1 5 sick a1 29 sick a1 7 healthy b2 2 sick c1 8 healthy c2 31 healthy b2 9 healthy d2
my code is:
> metadata_sorted$Group <- factor(metadata_sorted$Group)
> metadata_sorted$Condition <- factor(metadata_sorted$Condition)
> col_data_sorted <- DataFrame(
+ Condition = metadata_sorted$Condition,
+ Group = metadata_sorted$Group,
+ row.names = metadata_sorted$Sample
+ )
> col_data_correct_order <- col_data_sorted[match(colnames(filtered_count_matrix), rownames(col_data_sorted)),]
> if(!all(rownames(col_data_correct_order) == colnames(filtered_count_matrix))) {
+ stop("There is still a mismatch between the colData and countData columns.")
+ }
>
> dds <- DESeqDataSetFromMatrix(countData = filtered_count_matrix,
+ colData = col_data_correct_order,
+ design = ~ Condition + Group)
> dds <- DESeq(dds)
> rlog_transformed <- rlog(dds, blind = FALSE)
> vst_transformed <- vst(dds, blind = FALSE)
> head(assay(rlog_transformed))
resultsNames(dds)
res <- results(dds, contrast=c("ConditionNormal.Groupa1", "ConditionHealthy.Groupa1"))
Error:
Error in checkContrast(contrast, resNames) :
all elements of the contrast as a list of length 2 should be elements of 'resultsNames(object)'
I will be heartily thankful to you to help me to correct the design and perform ...
In limma it is showing same error for contrasts
