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Question: DESeq2 Fatal error
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gravatar for premraj.preeti
4 days ago by
premraj.preeti • 10
premraj.preeti • 10 wrote:

I am using DESeq2 to find deferentially expressed genes from count tables.

My Input files are feature counts generated using featurecounts

I had originally 6 samples (3 adults and 3 fetal), first using HISAT2 I performed alignment, then did QC using FATSQC and then counted the features of gene expression using featurecounts.

Now I am using DESeq2 to determine differentially expressed features. In this factor 1 I have named as adult and selected the feature count output for 3 adult samples and factor 2 named as fetal and selected the feature count output for 3 fetal samples.

I am getting the following error

primary factor: Gene_Expression

Fatal error: An undefined error occurred, please check your input carefully and contact your administrator. Error in data.frame(..., check.names = FALSE) : arguments imply differing number of row

Please help where I am going wrong
galaxy • 53 views
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modified 4 days ago by Flow • 100 • written 4 days ago by premraj.preeti • 10
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gravatar for Flow
4 days ago by
Flow • 100
Flow • 100 wrote:

I anticipate that either the input data is not correct for DESeq or the setting. So first check if your count/input data generated by featurecounts has the same features, i.e., the row names must be identically for all samples in your DESeq setup. So check if you used the same annotation file in featurecounts for all of your samples.

The second case, the setup: I think you want to find differentially expressed features between adult and fetal. So based on DESeq in Galaxy set one factor, e.g, "stage" and then select you adult samples as the first factor level "adult" and your fetal samples as second factor level "fetal".

Hope that helps
ADD COMMENT • link written 4 days ago by Flow • 100

Thanks for the reply. I did check all the rows are same for both samples and did the settings as above but now I am getting the following error.

primary factor: Stage

Error: ncol(countData) == nrow(colData) is not TRUE

Any suggestions

ADD REPLY • link written 4 days ago by premraj.preeti • 10

That seems odd ... maybe set the option "Files have header?" to No ... maybe that helps

ADD REPLY • link written 2 days ago by Flow • 100
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