User: n.anuragsharma

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Posts by n.anuragsharma

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Comment: C: Calculating z-scores using edgeR's fitted values (output of glmQLFit)
... As a continuation, would it be erroneous to average the log2 CPM values of replicates (after I have ascertained that there is indeed greater difference between samples rather than replicates)? ...
written 8 weeks ago by n.anuragsharma20
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Comment: C: Calculating z-scores using edgeR's fitted values (output of glmQLFit)
... Much appreciated, thank you. ...
written 8 weeks ago by n.anuragsharma20
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Calculating z-scores using edgeR's fitted values (output of glmQLFit)
... From what I can find in papers, heatmaps using RNA seq data are created in several ways: using log-fold changes, z-scores, etc. The edgeR vignette states: > Inputing RNA-seq counts to clustering or heatmap routines designed for microarray data is not straight-forward, and the best way to do thi ...
R rna-seq edger written 9 weeks ago by n.anuragsharma20 • updated 8 weeks ago by Gordon Smyth1.3k
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Creating a score for gene-ontology representation
... I have a group of genes (belonging to a certain development pathway, eg. known to increase trichome number) and their expression data from RNA seq. I have the log2 fold changes of each sample (3 mutants) relative to the control (wildtype) as computed by the edgeR package. I have been tasked with cr ...
R scaling rna-seq normalisation written 10 weeks ago by n.anuragsharma20 • updated 10 weeks ago by Jean-Karim Heriche21k
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Comment: C: Interpretation of RNA seq pipeline in a paper
... I understand. However, I have a line here from the paper which adds to my confusion: "We first adopt a highly stringent pair-wise comparison method5, in which a gene with a much higher RPKM (reads per kilobase million) value in one domain than all the other 8 domains (log2FC > 1, false discovery ...
written 10 weeks ago by n.anuragsharma20
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Interpretation of RNA seq pipeline in a paper
... The paper I refer to is: https://doi.org/10.1038/s41467-018-08083-z A couple of snippets from the results & methods section: > "We **first adopt** a highly stringent pair-wise comparison method5, in which ***a gene with a much higher RPKM (reads per kilobase million) value in one domain th ...
R rna-seq edger written 10 weeks ago by n.anuragsharma20 • updated 10 weeks ago by colin.kern780
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Comment: C: Require comprehensive tutorials for PCA analysis of microarray
... Thank you for your response! I will elaborate along with some more questions if that's okay: 6) Is there a way to find out which are the set of genes in my microarray/RNA seq that are contributing the most to the observed variation? I think I have the answer to this from your tutorial- plotloadings ...
written 11 weeks ago by n.anuragsharma20
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Require comprehensive tutorials for PCA analysis of microarray
... I've been exploring PCA analysis of a microarray experiment. I have a microarray of two genotypes of transgenic plants induced under 6 different time points. I have the following exploratory questions I would like answered with the PCA. 1) where does most of the variation lie? 2) which time points ...
R pca microarray written 11 weeks ago by n.anuragsharma20 • updated 11 weeks ago by Kevin Blighe53k

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