User: m.fletcher

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m.fletcher10
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New User
Location:
Germany
Last seen:
1 year, 1 month ago
Joined:
2 years, 9 months ago
Email:
m*********@dkfz.de

Posts by m.fletcher

<prev • 5 results • page 1 of 1 • next >
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Gene Set Testing or GSEA for functional annotation of co-expressed ncRNA and coding genes
... Hello, I have a question about the appropriate manner in which to do a gene set test. The aim is to functionally annotate a list of non-coding genes, using guilt-by-association with known coding genes, based on gene expression correlation. Briefly: I have a list of non-coding genes (both known EN ...
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Comment: C: Visualising effects of observation/sample weights in differential expression ana
... Dear James, Thank you for the references, although your second link doesn't work! I'm trying your suggestion of plotting the weights also, although there doesn't seem to be any association of up-/down-weighting of samples and where they fall on my MDS (within a subgroup, between two subgroups, etc ...
written 2.7 years ago by m.fletcher10
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Visualising effects of observation/sample weights in differential expression analysis
... Hello, I'm working on a RNA-seq differential expression analysis on human samples, and have been trying to understand the effect of the various packages that allows the weighting of samples or features - e.g. voom's sample quality weights, or edgeR-robust's implementation of observation weights. I ...
limma edger sva voom written 2.7 years ago by m.fletcher10 • updated 2.7 years ago by Matthew Ritchie660
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Comment: C: DESeq2 design matrix for 6 groups
... Thank you very much for the suggestions! I will, of course, try both approaches and see which gives the more sensible results. ...
written 2.8 years ago by m.fletcher10
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DESeq2 design matrix for 6 groups
... Hello,   I have a question about the best DESeq2 experimental design matrix for my dataset.   I am working with 75 RNAseq samples from the same tissue, but classified in various subtypes as follows: 5x normal tissue (group A), which I use as the reference/denominator in the analyses. 22x ear ...
rnaseq deseq2 design and contrast matrix written 2.8 years ago by m.fletcher10 • updated 2.8 years ago by Michael Love14k

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