User: bcbio_uk

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bcbio_uk10
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United Kingdom
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2 years, 7 months ago
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Posts by bcbio_uk

<prev • 7 results • page 1 of 1 • next >
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WGCNA "bicor" correlation
... Hello, I have a question regarding the appropriate correlation to use for smaller sample sizes when creating an adjacency matrix in WGCNA. I have 8 samples in my condition, and although these are not ideal numbers for WGCNA, I would like to give this a try. I was recommended using the bicor correla ...
wgcna bicor written 3.8 years ago by bcbio_uk10
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Comment: C: Limma - discrepancy in number of significant genes
... I did yes, I just didn't paste that part of the code as I wanted to keep it simple. Thank you for checking. -Akul ...
written 4.1 years ago by bcbio_uk10
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Comment: C: Limma - discrepancy in number of significant genes
... Dear James, Thank you very much for your detailed response. It makes a lot of sense and explains why I'm seeing more significance. This was exactly what I was looking for.  Thanks, Akul ...
written 4.1 years ago by bcbio_uk10
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Comment: C: Limma - discrepancy in number of significant genes
... Dear svlachavas, Thank you very much for your quick and very helpful reply. I've tried your suggestions (without the 'trend' attribute for now), and I get the same exact 3 gene lists for coef1, coef2 and coef3 that I got when I used my code: > design <- model.matrix(~0 + Treat) > fit < ...
written 4.1 years ago by bcbio_uk10
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Limma - discrepancy in number of significant genes
... Dear all, I have a question about differential gene expression calculation using limma. I have two disease groups - D1 (n=6) and D2 (n=7) that I have first compared to each other and obtained about 30 genes that have adj.P-value < 0.05. Please see the code that I've used below. > design < ...
microarray limma linear model differential gene expression written 4.1 years ago by bcbio_uk10 • updated 4.1 years ago by James W. MacDonald50k
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Comment: C: Limma: advice needed for best approach for joint paired and unpaired analyses in
... Hi Aaron,     Thanks very much for your quick reply. My analysis is indeed using the four-group design as you pointed out. This is exactly the kind of analysis I was after, so I could utilise all of my samples, but still keep the paired structure for samples that do have their corresponding pairs ...
written 4.7 years ago by bcbio_uk10
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Answer: A: Limma: advice needed for best approach for joint paired and unpaired analyses in
... Hi Aaron and Guido, I have a similar issue in my dataset. My experimental design is similar to the "9.7 Multi-Level Experiments" design in the Limma user guide (http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf). Except I have some subject that are paired and ...
written 4.7 years ago by bcbio_uk10

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