User: bekah

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bekah0
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Posts by bekah

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Estimating group-specific dispersion in DESeq2
... ​This was the pca created from logtransformed data using blind = FALSE to make sure biological variation from treatment was not smoothed out excessively. Colours are the experimental treatment groups (i.e. 5 replicates per treatment). I think that the dispersal is too varied and independent pairwi ...
written 2 days ago by bekah0
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Comment: C: IHW Package for R 3.2.5
... cheers - is all sorted, managed to call the latest R version and run as admin to get the packages needed to install  ...
written 3 days ago by bekah0
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Comment: C: Estimating group-specific dispersion in DESeq2
... Hi Michael - Is there a cut off for differences in dispersions as to whether the contrast function is suitable to use over testing pairwise groups by inputting the pairs of data in independently? ...
written 3 days ago by bekah0
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Comment: A: IHW Package for R 3.2.5
... Cheers- I'll see what versions are available,! ...
written 7 days ago by bekah0
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IHW Package for R 3.2.5
... Hiya, I'm trying to find a version of IHW that is compatible with R 3.2.5 in which I am running DESeq2, but haven't had any luck - is there an alternative package that does a similar function that I could use instead that you would recommend please? Best wishes Rebekah ...
deseq2 ihw written 7 days ago by bekah0
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Comment: C: Different results using DESeq2
... Ah thanks that makes sense! ...
written 11 days ago by bekah0
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Comment: C: Different results using DESeq2
... I'm a little bit confused - is there a benefit for having the same single dispersion value for the genes across all samples, as in is it better to be consistent (therefore having a consistent sensitivity to selecting sig, DE genes) if wanting to eventually look at the different log counts across all ...
written 11 days ago by bekah0
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Comment: C: Different results using DESeq2
... Cheers - sorry I had missed that entirely when I read the vignette the first time! ...
written 12 days ago by bekah0
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Comment: C: Different results using DESeq2
... Trinity seems to make a new matrix containing just the data from the two pairs of treatments to input into DESeq2 - is it better to use this method or use the entire dataset and use the contrast function in the script? ...
written 12 days ago by bekah0
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Different results using DESeq2
... Hiya, ​I am finding that if I am inputting my data in one count matrix and calling to contrast two different treatments from the four (each with 5 sample replicates) using the contrast function in DESeq2 that I get different differential expression results to that if I look at the samples using the ...
deseq2 written 4 weeks ago by bekah0 • updated 4 weeks ago by Michael Love11k

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