DIANE fails when DE analysis is performed

[kostasgalexiou]

Hi,

When I launch DIANE locally and then try to perform the DE analysis, I get the following error.

Warning in edgeR::DGEList(counts = tcc$count, lib.size = tcc$norm.factors,  :
  norm factors don't multiply to 1

Warning in estimateDisp.default(y = y$counts, design = design, group = group,  :
  No residual df: setting dispersion to NA

Warning: Error in glmFit.default: NA dispersions not allowed```

Is it related to my data or it has to do with something else? Please let me know so I can provide you with some extra information.

Thanks

[Alexandre-So]

Hello,

This can indeed be related to your data. Could you send me your count matrix at "alexandre.soriano@cirad.fr", so I can try to reproduce this error ?

This will of course remain private.

Best,

[kostasgalexiou]

Hi Alex,

I found the error! I did not indicate replicates in the column header. Because of this, DIANE thinks that I have 1 sample with 12 replicates.

Now everything runs smoothly...

Best Kostsa

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Konstantinos Alexiou, PhD Bioinformatician

IRTA Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB Campus UAB, Edifici CRAG 08193 Bellaterra (Cerdanyola del Vallès)

@. - @. Tel: +34 93.563.66.00 ext. 3360 www.cragenomica.eshttp://www.cragenomica.es/ - www.irta.cathttp://www.irta.cat

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De: Alexandre Soriano @.> Enviado: viernes, 6 de octubre de 2023 11:26 Para: OceaneCsn/DIANE @.> Cc: Alexiou, Konstantinos @.>; Author @.> Asunto: Re: [OceaneCsn/DIANE] DIANE fails when DE analysis is performed (Issue #46)

Hello,

This can indeed be related to your data. Could you send me your count matrix at @.**@.>", so I can try to reproduce this error ?

This will of course remain private.

Best,

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[Alexandre-So]

Hi Kostsa,

Indeed, that was the main error !

There is also another small problem in your count matrix. If you look at the 5 last lines, you can see that it concerns global information about the counts.

You should remove these lines.

Best, Alexandre