User: marc.osullivan

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Posts by marc.osullivan

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Comment: C: Recommendations for normalisation post-deseq2
... Thanks for your feedback on this I've now read up on rlog and vsd in the vignette, can I confirm that the VST is a transformation after normalisation according to size factors. As this is my interpretation from your vignette below: "Above, we used a parametric fit for the dispersion. In this case, ...
written 9 weeks ago by marc.osullivan0 • updated 9 weeks ago by Michael Love22k
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Recommendations for normalisation post-deseq2
... Hello, Can anyone here recommend any posthoc normalisation steps following deseq2 before generating Partial Least Squared Discriminant Analysis (PLSDA) and VIP (Variance of Importance Plots)? I presume it's not appropriate to just perform this code and use it to generate a PLSDA with these counts? ...
normalization deseq2 posthoc written 9 weeks ago by marc.osullivan0
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NAs create inaccuracies with BH corrections in deseq2
... I've just started using deseq2 and have noticed that some p adjusted values are appearing as NA in my output CSV. The issue with this is the package excludes any genes with an adjusted p-value = NA from the total ranking count and therefore generates an inaccurate adjusted p-value. i.e. total genes ...
deseq2 written 10 weeks ago by marc.osullivan0 • updated 10 weeks ago by Michael Love22k
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Script for fold change in DESeq for count data with 2 groups
... I'm new to both R and DESeq2 and I have a script to work off but this will only generate Log2 fold change? Does anyone know what script to add to calculate untransformed fold change to my read counts? I've attached the script below. <------------------------------------------------------------- ...
rnaseq deseq2 written 10 weeks ago by marc.osullivan0 • updated 10 weeks ago by Michael Love22k

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