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 5 weeks 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 6 weeks 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 8 weeks 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 8 weeks 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 9 weeks 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 11 weeks 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 12 weeks 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 3 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 3 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 3 months ago by Jane Merlevede90

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