Hi,

I am new to R and DESeq2 package for RNAseq analysis. I am trying to analyze the read counts of 2 samples (M1, M2) as 3 biological triplicates (M11, M12, M13 and M21, M22, M23). I read the files into R as .csv but when I try to create a dds I get the following error. Could you please help me? Is something wrong with my data format?

> Read_Counts <- read.csv("Read Counts.csv", header =  TRUE)
> head(Read_Counts)
       ï..Gene_ID SP_18 SP_23 SP_28 SP_20 SP_25 SP_30
1 ENSG00000000003    88    45    30    70   100   151
2 ENSG00000000419   604   920   828   905   596  1047
3 ENSG00000000457   258   242   153   252   119   135
4 ENSG00000000460    77    70    51   152    76    75
5 ENSG00000000938  3074  3672  2948  5560  5434  7641
6 ENSG00000000971  4521   115    55    42     1     0


> Meta_Data <- read.csv("Meta Data.csv", header = TRUE)
> head(Meta_Data)
  ï..Sample_ID Condition CellType
1        SP_18      M1_1       M1
2        SP_23      M1_2       M1
3        SP_28      M1_3       M1
4        SP_20      M2_1       M2
5        SP_25      M2_2       M2
6        SP_30      M2_3       M2

> dds <- DESeqDataSetFromMatrix(countData = Read_Counts, colData = Meta_Data, design = ~ CellType)
Error in DESeqDataSetFromMatrix(countData = Read_Counts, colData = Meta_Data,  : 
  ncol(countData) == nrow(colData) is not TRUE.

Hi hamidreza, to solve the problem, convert ï..GeneID column in ReadCounts as row names. In ReadCounts there are 7 columns (GeneID + 6samples), in MetaData there are 6 rows (6 samples), so ncol(countData) == nrow(colData) is not TRUE.