User: Jane Merlevede

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Posts by Jane Merlevede

<prev • 86 results • page 1 of 9 • next >
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Answer: A: Gene clusters based on gene expression across samples
... Any feedback on gene clustering using classical clustering methods? ...
written 11 months ago by Jane Merlevede90
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Answer: A: Gene clusters based on gene expression across samples
... Well, I tried WGCNA and indeed, it seems to fit my needs. Thank you. I would like to test some simpler clustering methods, like methods based on medoid partitioning. Using kmeans(), on 2 distinct datasets, with 5 or 10 clusters, I got several clusters (between 2 or 4) containing a single gene. Did ...
written 11 months ago by Jane Merlevede90
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Comment: C: Gene clusters based on gene expression across samples
... No, I did not know. I will take a look, thank you ...
written 12 months ago by Jane Merlevede90
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Gene clusters based on gene expression across samples
... Dear all, Using an RNASeq experiment of 16 samples, I would like to cluster genes, and not samples. My aim is to identify subsets of genes that behave similarly across the samples, which could be possible using a good metric (maybe correlation?). After a normalization performed with DESeq2, I comp ...
clustering kmeans gene expression written 12 months ago by Jane Merlevede90
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Comment: C: Sample-to-sample distance matrix using heatmap.2
... I took few days to try it, indeed pheatmap seems clearer to actually be sure of the measure used on rows and columns. Thank you ...
written 12 months ago by Jane Merlevede90
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Comment: A: Sample-to-sample distance matrix using heatmap.2
... Thank you for your answer Michael. I have seen pheatmap(), will probably try it, but I prefer the simpler heatmap.2() plot. Nevertheless, my question remains: Since you give as input a matrix in which elements are already correlations (or euclidean distances), for what will be used the distance t ...
written 13 months ago by Jane Merlevede90
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Sample-to-sample distance matrix using heatmap.2
... Dear all, I would like to plot a distance matrix (a correlation matrix) obtained from correlations between gene expression from an RNASeq experiment. The samples were analysed using DESeq2 and besides the differential expression analysis, I am plotting the relationships between samples and genes an ...
deseq2 heatmap.2 gplots written 13 months ago by Jane Merlevede90
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Comment: C: DESeq2 - experimental design with 2 variables
... Thank you for your help. Yes, I will try to clarify these points. ...
written 13 months ago by Jane Merlevede90
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Comment: C: DESeq2 - experimental design with 2 variables
... Thank you for your reply. I guess, in the estimation of the average of the low intensity, the sample size is taken into account? There are 4 samples in CellLine1 and 2 in the other one. Since there are less samples in the CellLine1, I want them to contribute less in the model.   Sorry, I don't se ...
written 13 months ago by Jane Merlevede90
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Comment: A: DESeq2 - experimental design with 2 variables
... If I may ask one more thing, I would like a confirmation: To look for the differences between the 5 controls and the 6 tumors with low intensity (whatever the cell type), I think I should use the contrast:   resultsNames(ddsFinal) [1] "Intercept" "Intensity_CellLinesCDX_1_Lo ...
written 13 months ago by Jane Merlevede90

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Popular Question 17 months ago, created a question with more than 1,000 views. For DESEq2 - Why is "my gene" not differentially expressed?

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