I have 16 samples and 4 treatment groups
my transcripts are quantified by salmon Galaxy
I used Transcript-gene association mapping : Homo_sapiens.GRCh38.cdna.all.fa).
I generated successfully read counts and TPMs using lengthScaledTP (RNA-seq Data information attached)
In Data pre-processing, quality control plots are generated and low expressed transcripts and genes were filtered based on expression mean-variance trend. PCA plots were generated and batch effect removed using RUVr method.
However, at step 4 of Data Normalisation and when I run and plot distribution (TMM, RLE or upperquartile) I have this error message : An error has occurred. Check your logs or contact the app author for clarification.
Even if I skip this step and I generate the contrast group, when I run the 3D analysis the page freezes and there is no data generated and from the 15601 genes none is DE .....
Thank you for your help !
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Hello,
I have 16 samples and 4 treatment groups my transcripts are quantified by salmon Galaxy I used Transcript-gene association mapping : Homo_sapiens.GRCh38.cdna.all.fa). I generated successfully read counts and TPMs using lengthScaledTP (RNA-seq Data information attached) In Data pre-processing, quality control plots are generated and low expressed transcripts and genes were filtered based on expression mean-variance trend. PCA plots were generated and batch effect removed using RUVr method. However, at step 4 of Data Normalisation and when I run and plot distribution (TMM, RLE or upperquartile) I have this error message : An error has occurred. Check your logs or contact the app author for clarification.
Even if I skip this step and I generate the contrast group, when I run the 3D analysis the page freezes and there is no data generated and from the 15601 genes none is DE .....
Thank you for your help !
Screenshots
Additional context Add any other context about the problem here.