User: chris86

gravatar for chris86
chris86340
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UCL, United Kingdom
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I am a post-doc data analyst working in Rhuematoid Arthritis research in London.

Posts by chris86

<prev • 138 results • page 1 of 14 • next >
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Answer: C: Using tximport to convert a dataframe consisting of tpm to counts for use with l
... You wouldn't use tximport to convert a matrix of TPM counts into CPM. The question of using TPMs for differential expression with limma has been covered before here: https://support.bioconductor.org/p/98820/ ...
written 19 hours ago by chris86340
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Comment: C: Diferential expresion analysis between different microarray platforms
... I don't think you should do that. ...
written 15 days ago by chris86340
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Comment: C: Differential gene expression of longitudinal data
... I think you could look into mixed models with repeated measures instead of ANOVA, they can handle missing data I think. Another option is data imputation prior to doing a repeated ANOVA, but I think the above option is usually preferred. ...
written 20 days ago by chris86340
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Comment: C: Heat MAP TPM
... I am not sure I understand your question. You have 4 replicates, if these are in the matrix that goes into the heatmap function they will be plotted. If you want to average by column to combine replicates, just could google for that.   ...
written 28 days ago by chris86340
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Answer: A: Heat MAP TPM
... Your saying rather than using log2FC, but are you sure that is what you mean? You are currently running your heatmap function on z score normalised TPMs. I would first take log(TPM+1) before doing the z score. That should be approx normally distributed which is required for doing z scores. Other ...
written 29 days ago by chris86340
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Answer: A: Choosing genes for clustering
... This is common. There are ways of calculating cluster strength and stability which you could apply to different numbers of DE genes, however, this is a danger of being a bit too selective here. I would just test a few different numbers, 30, 50, 100, etc. Then choose what you need, it depends on what ...
written 10 weeks ago by chris86340
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Answer: A: Bayesian Network analysis of gene regulatory relationship
... As far as I understand it, bayesian networks are just an alternative to correlation networks (WGCNA) or mutual information networks (ARACNE). I think your false positive rate would probably be high, but it is a valid way of finding candidates, whether it is methodologically sound.... I think that is ...
written 10 weeks ago by chris86340
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Comment: C: Some doubts about the limma package
... No the primary research papers are what you need to read buddy. ...
written 3 months ago by chris86340
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Comment: C: Some doubts about the limma package
... You need to read the limma papers, just search for 'limma linear models' in google scholar or anything like that. Limma uses normalised data, like quantile normalised, you should be able to normalise within the package. ...
written 3 months ago by chris86340
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Answer: A: When is centering and scaling needed before doing hierarchical clustering?
... Scaling is only necessary when you are combining data of different types, like height and weight for example. Centering is done in principal component analysis for instance, it is not needed for clustering as it will not effect the results. You could also consider trying kmeans with the silhouette ...
written 3 months ago by chris86340

Latest awards to chris86

Popular Question 5 months ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Autobiographer 18 months ago, has more than 80 characters in the information field of the user's profile.
Supporter 19 months ago, voted at least 25 times.
Scholar 19 months ago, created an answer that has been accepted. For A: Apply the plotPCA function in DESeq2 package to quantitative MS-based data
Centurion 19 months ago, created 100 posts.
Scholar 19 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Student 19 months ago, asked a question with at least 3 up-votes. For Limma camera function never gives any differentially expressed gene sets
Scholar 19 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes

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