User: Jane Merlevede

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Posts by Jane Merlevede

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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 1 day 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 1 day ago by Jane Merlevede90 • updated 1 day ago by James W. MacDonald44k
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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 6 days 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 25 days 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 27 days 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 6 weeks 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 6 weeks 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 6 weeks ago by Jane Merlevede90
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Comment: A: DESeq2 - experimental design with 2 variables
... Ok, thank you for your answer ...
written 7 weeks ago by Jane Merlevede90
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DESeq2 - experimental design with 2 variables
... Dear all, I have trouble writing my design formula for an RNASeq experiment of 16 samples. There are 5 controls and 11 tumors. The tumors correspond to 2 cell lines and have either Low or high intensity: Sample name Intensity CellLine 1 CDX_1_1 Low_BLI CDX_1 2 CDX_1_2 Low_BLI CDX_1 ...
deseq2 multiple factor design written 7 weeks ago by Jane Merlevede90

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