Error while doing EdgeR fro miRNA Seq analysis
Hi all,
I am presently doing miRNASeq analysis. I have come across an error while doing the differential expression analysis. Could anyone please help me to rectify this error?? I am pasting the commands below;
Got 3 samples, and got: 3 data fields.
Header: miRNA ID Early Stage Stage III
Next: hsa-miR-6829-5p 7 56
-shifting sample indices over.
$VAR1 = {
'Early Stage' => 1,
'Stage III' => 2
};
$VAR1 = {
'SRR7189569' => [
'Early'
],
'SRR7189579' => [
'Stage'
]
};
Contrasts to perform are: $VAR1 = [
[
'SRR7189569',
'SRR7189579'
]
];
Error, cannot determine column index for replicate name [Early]$VAR1 = {
'Early Stage' => 1,
'Stage III' => 2
};
Thank you in advance
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nivya.james2016 •
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nivya.james2016 •
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This doesn't look like traditional edgeR within the R environment. Can you clarify how you're executing edgeR?
Yes sure
This was my command for executing edgeR
Why are you using Trinity? If you want to use edgeR, just use edgeR.
Trinity has a plethora of helper scripts, wrapping all kinds of analyses. Although they can be helpful if they work properly, if they fail, they only add complexity to the debugging task.
@nivya.james2016: the script is trying to assign which counts matrix columns should be assigned to each treatment. Apparently you used spaces in counts matrix column names and / or treatments, my guess is these spaces are causing incorrect parsing of names. Try replacing the spaces by underscores, or just remove them.