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

…

----- 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.es<http://www.cragenomica.es/> - www.irta.cat<http://www.irta.cat>

________________________________ 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, — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/OceaneCsn/DIANE/issues/46*issuecomment-1750274816__;Iw!!D9dNQwwGXtA!SLEjYSfzCqUFjGKrRnNIn9_LQyQoWtGGy2H_5wjDyzPo_3G8MKV10Kv-pO809Hr56DAG9WS9s2_DvgR9IhyRLM7vNPT5PvgCmw$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AM4FYKFCNRAS4FAIOXKWMK3X57FF5AVCNFSM6AAAAAA5VQTGM2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJQGI3TIOBRGY__;!!D9dNQwwGXtA!SLEjYSfzCqUFjGKrRnNIn9_LQyQoWtGGy2H_5wjDyzPo_3G8MKV10Kv-pO809Hr56DAG9WS9s2_DvgR9IhyRLM7vNPQ6ilqNDA$>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[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