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 10 months 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 10 months 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 10 months 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 10 months 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 10 months ago by bekah0
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Comment: C: Different results using DESeq2
... Ah thanks that makes sense! ...
written 10 months 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 10 months 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 10 months 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 10 months 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 11 months ago by bekah0 • updated 11 months ago by Michael Love16k

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