DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Entering edit mode
Patadù ▴ 10
Last seen 3 days ago
The Netherlands

I am new to RNAseq and started to analyze my dataset using DESeq2. I first run the DESeqDataSetFromMatrix function and found the error message

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

In addition, if I run the following code I get this warning:

all(colnames(HitCount) == myCondition$SampleID)
Warning message:
In colnames(HitCount) == myCondition$SampleID :
  longer object length is not a multiple of shorter object length

I then searched online and arranged my code as follow:

myCondition <- read_excel("ConditionTable.xlsx")

HitCount <- read_excel("HitCounts_30mpi.xlsx", col_names = TRUE,
                       col_types = c("text", "numeric", "numeric",
                                     "numeric", "numeric", "numeric",
                                     "numeric", "numeric", "numeric", 
rownames(HitCount) <- HitCount[,1]
HitCount <- HitCount[,-1]

all(colnames(HitCount) == myCondition$SampleID)


dds <- DESeqDataSetFromMatrix(countData = HitCount,
                              colData = myCondition,
                              design = ~ Condition)

dds <- DESeq(dds)

However, I do get the following error when running rownames(HitCount) <- HitCount[,1]:

Error in .rowNamesDF<-`(x, value = value) : 
invalid lenght in 'row.names'

This does not stop R to in the calculation but I get in my results that the row names are changed in numbers. Do you know how I can keep the original row names and having DESeqDataSetFromMatrix TRUE?

This is a piece of my excel file:

Gene_ID CTRL_1 CTRL_2 CTRL_3 SXM_1 SXM_2 SXM_3 XS_1 XS_2 XS_3
VDAG_00XX1 661 558 555 509 325 338 526 611 419 2

VDAG_00XX2 1920 1545 1457 2033 1160 1231 1691 1689 1496 3

VDAG_00XX3 568 568 514 946 718 728 1805 1920 1549 4

VDAG_00XX4 6774 6676 7036 5335 4079 3917 8557 9658 7973

DESeq2 • 751 views
Entering edit mode
Last seen 2 hours ago
United States

Starting from the very top, do you understand the error? You need to provide sample info that matches 1-to-1 the columns of the counts matrix. You had unequal samples in the counts matrix and in the sample info table, indicating a problem.

Entering edit mode

Hi Michael,

Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only had the different treatment, CTRL, SXM, XS. I found out that I had to start from the second colum of my .csv file. In this way the condition and the matrix file matched. Now I do not get anymore that error and when I do run the code, GeneID names are kept.


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