User: Wuschel
Wuschel • 120
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Posts by Wuschel
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... I am looking for Plant (plastid vs. total) Transcriptomics / RNA-Seq lecture notes to self-study.
Could anyone help me with useful resources (books/university lecture notes) ...
written 6 weeks ago by
Wuschel • 120
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... Thank you Kevin,
I have a proteomics timecourse experiment of two genotypes vs WT. Would like to see the enrichment of these proteins for different metabolomics pathways. Something similar to below images.
Later I am going to perform RNAseq, so preferably would like to visualize the data in the sa ...
written 10 weeks ago by
Wuschel • 120
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... Very kind of you Ariel. Looking forward to it. If I come across any solution will keep you informed too. Thank you. ...
written 10 weeks ago by
Wuschel • 120
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... Does anyone have experience in integrating and visualizing RNASeq / Proteomics data for metabolomics pathways?
Is there any user-friendly R package or free software available for this type of analysis?
Would be grateful if you could direct me to the right place with accessible examples/tutorials. ...
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... I am unable to get gene names to heatmap in a readable font (> 600 genes). Is there any way that I could export clustering genes to a separate file (e.g. csv)?
plot_heatmap(df, type = "centered", kmeans = TRUE,
k = 6, col_limit = 2, show_row_names = T) ...
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... [calculate fold change (FC)][1]
When comparing these log transformed values, we use the quotient rule of logarithms:
>log(A/B) = log(A) - log(B)
>log(A) = 4
>log(B) = 1
>Therefore:
>log(A/B) = 4 - 1
>log(A/B) = 3 This gives a 3-fold change.
Please note that in this case we ...
written 12 weeks ago by
Wuschel • 120
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... Thank you @geek_y.
After getting log2FC; e.g. -3.3, how can we calculate the % of change? is that %change = (Change/Original) x 100 ?
...
written 3 months ago by
Wuschel • 120
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9 follow
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... I am trying to understand Gene expression data analysis. Could someone the percentage of change of the GE calculating from log2 fold change (L2FC)?
> FoldChange = μ_Treatment / μ_Control
>
> log2FC=Log2(μ_Treatment)-Log2(μ_Control)
...
written 3 months ago by
Wuschel • 120
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... Thank you, Kevin. Yes, I had a look at that. But I want to perform it in another standard statistical procedure. After data Imputation step from DEP package. ...
written 3 months ago by
Wuschel • 120
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... Hi Kevin,
Yes. These are my data and I've normalized. I used DEP Package in bioconductor. ...
written 3 months ago by
Wuschel • 120
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