User: crouch.k

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crouch.k10
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Posts by crouch.k

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Order of operations in RNAseq analysis
... Just to close this, removing the samples that I had decided not to include prior to building the model solved my issues. After that, the signal remained fairly consistent no matter what I did. I suspect these samples that were prepared differently were creating noise that was masking the signal we ...
written 4 months ago by crouch.k10
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Comment: C: Order of operations in RNAseq analysis
... Yeah, I was assuming there wasn't a "correct" answer, but I was concerned because the way samples clustered in the exploratory analysis was changing depending on the order I did things in. Input from outside is useful because I was getting to the point of over thinking and confusing myself so thank ...
written 5 months ago by crouch.k10
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Comment: C: Order of operations in RNAseq analysis
... Thanks for your responses. Your suggestion to include the batch in the design formula is what I usually do for differential expression. I had been led to believe that I had to remove it rather than model it for wgcna, but thinking about it, as long as I can't see it in the PCA it probably doesn't ...
written 5 months ago by crouch.k10
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Order of operations in RNAseq analysis
... Hi all, I have some RNAseq data and I would like to take the results forward to build a network based on expression correlation (wgcna or similar). I have several steps that I need to carry out: - normalise data - transform data - subset data (not everything in the dataset is useful for the i ...
wgcna deseq2 rna-seq written 5 months ago by crouch.k10 • updated 5 months ago by Kevin Blighe32k
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Comment: C: Finding novel domains in a group of proteins
... Thanks for the useful suggestions! I will have a play with some of these. Thanks so much for the offer to have a go with your software too. I'll drop you an email. ...
written 9 months ago by crouch.k10
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Comment: C: Finding novel domains in a group of proteins
... Thanks! Yes I will have a play with MEME. What I meant by the naivety of MSA is that at the moment I don't have any idea what a potential domain might look like or where it could be. I think I really need to try to refine domain boundaries first, even if not precisely, and then start looking at M ...
written 9 months ago by crouch.k10
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Finding novel domains in a group of proteins
... I have been posed the following problem by a collaborator and I could use some advice on how to approach it: The collaborator works with a non-model organism. He is interested in how a particular protein binds to other proteins. He has done a pulldown with his protein followed by Mass Spec, and h ...
genome gene alignment written 9 months ago by crouch.k10 • updated 9 months ago by jrj.healey8.8k
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Comment: C: Get FPKM across replicates without doing a differential expression
... Hi Thanks for the reply. Yes, I am aware of the pitfalls of FPKM and have used DESeq2 for differential expression for a long time. In this case, I am working with a non-model organism that has a very unusual genome architecture. Specifically, genes are transcribed in large polycistronic units t ...
written 13 months ago by crouch.k10
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Get FPKM across replicates without doing a differential expression
... Hi, I am trying to perform a within-sample analysis of expression data using FPKM - essentially I want to be able to rank my genes. I am not doing differential expression. I have 3 biological replicates of my sample. What I would like to be able to do is generate an FPKM for each gene that is re ...
fpkm dna-seq rna-seq written 13 months ago by crouch.k10 • updated 13 months ago by Kevin Blighe32k

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