Question: DESeq2 Trouble shoot
0
gravatar for jaqx008
2.0 years ago by
jaqx00890
jaqx00890 wrote:

Hey all, I recently succesfull rna DESeq2 analysis succesfully but I mad changes to my count table and wanting to rerun it in R. I encountered an error as before and followed all the steps I have written down in my documentation but still getting the error when I try to make dds. I could not figure out what I am doing wrong in either my count table or conditions table. both shown below. Error

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

Conditions.csv

Sample,Condition,Replicate
Untreated1,Untreated,1
Untreated2,Untreated,2
Untreated3,Untreated,3
Untreated4,Untreated,4
Treated1,Treated,1
Treated2,Treated,2
Treated3,Treated,3
Treated4,Treated,4

count.txt

    Untreated1  Untreated2  Untreated3  Untreated4  Treated1    Treated2    Treated3    Treated4
Bf_V2_1:1:797   0   0   0   0   0   0   0   0
Bf_V2_1:72:637397   3227    3149    3150    3085    4068    4019    4122    4075
deseq2 dds scatterplot • 989 views
ADD COMMENTlink modified 2.0 years ago by Devon Ryan98k • written 2.0 years ago by jaqx00890

The error message tells you explicitly what's wrong, pointing you to what you should investigate:

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

The number of columns in the countdata ncol(countData) doesn't match the number of rows in the sample info nrow(colData). Don't panic when you get an error message, but read it carefully.

ADD REPLYlink written 2.0 years ago by WouterDeCoster45k
1
gravatar for Devon Ryan
2.0 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

Look at the first row of Amphcts and coldata. It's likely that either coldata still has the header row as a normal row or that Amphcts has the row names as a column. Either one of those will cause this.

ADD COMMENTlink written 2.0 years ago by Devon Ryan98k

Thanks for your suggestion. have looked at the coldata and cts data. I have tried to adjust it in different ways but I am getting the same error and its frustrating. However, in my count data, if I remove the loci column, it generates my graph as expected, but I do need the loci info to be in the log2fold change information at the end.

ADD REPLYlink written 2.0 years ago by jaqx00890

The loci should be row names, not a column.

ADD REPLYlink written 2.0 years ago by Devon Ryan98k

Thanks I think I understand it better now. Thanks again

ADD REPLYlink written 2.0 years ago by jaqx00890
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