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User: tonja.r

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tonja.r40
Reputation:
40
Status:
New User
Location:
United Kingdom
Last seen:
2 years, 3 months ago
Joined:
3 years, 10 months ago
Email:
t*********@googlemail.com

Posts by tonja.r

<prev • 60 results • page 1 of 6 • next >
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RUVg or RUVs
... I have quite a strong batch effect in my data (paired design,i.e. first replicates of treated and control were done together and second replicates of treated and control also together). Additionally, I need to say that I am studying quite a moderate effect so ,that I expect a small number of genes t ...
ruvseq written 3.0 years ago by tonja.r40 • updated 3.0 years ago by g.atla0
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Comment: C: DESeq2 MA plot of encode data
... I edited my question with new plots and edgeR results. ...
written 3.1 years ago by tonja.r40
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squeezing of dispersion in the deseq2 and edger.
... In DESeq2 paper: edgeR [2,3] moderates the dispersion estimate for each gene toward a common estimate across all genes, or toward a local estimate from genes with similar expres- sion strength, using a weighted conditional likelihood.  However, as far as I understood the dispersion estimate in DESe ...
edger deseq2 written 3.1 years ago by tonja.r40 • updated 3.1 years ago by Michael Love22k
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Comment: C: DESeq2 MA plot of encode data
... Yes, I do compare them identically and I checked if I switched columns in one of the datasets and it is not the case. It is also a bit strange to me that the number of DE genes in dataset B is twice less then in dataset A. I also checked the read lengths in dataset A and it turned out that in the c ...
written 3.1 years ago by tonja.r40
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Comment: C: DESeq2 MA plot of encode data
... I edited my question by adding the plots you asked for. 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol. ...
written 3.1 years ago by tonja.r40
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DESeq2 MA plot of encode data
... Hello, I took encode data RNAseq from mouse G1E cell line and G1E treated with 24 hours of estradiol.  I had following data: dataset A G1E, 2 replicates, single end reads G1E-treated, 2 replicates, single end reads dataset B G1E, 2 replicates,paired end reads G1E-treated, 2 replicates, paired end ...
normalization edger deseq2 written 3.1 years ago by tonja.r40
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Comment: C: deseq2, edger different number of replicates and extraction kit
... What would be better: to analyze together the replicates that are at least from the same extraction kit and block for the sequencing protocol or to analyze everything separately and look at the intersections of the genes with FDR<0.05? ...
written 3.1 years ago by tonja.r40
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Comment: C: deseq2, edger different number of replicates and extraction kit
... edited my question ...
written 3.1 years ago by tonja.r40
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deseq2, edger different number of replicates and extraction kit
... 1.Would it be a potential bias if I have 2 replicates for one condition and 4 replicates for the other? Or would it better to use then only 2 replicates per condition? Dataset 1: cond A,  2 replicates cond B, 4 replicates   2.Also, in my another dataset I have 2 replicates extracted with Long Pol ...
edger deseq2 written 3.1 years ago by tonja.r40
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edger and deseq2 log2FC nornalization
... In the Microarray if the data is not center around 0 on MA-plots, it is normalized with LOESS. I was not able to find if edgeR performs something like loess normalization for log2Fold changes as it seems that the values are always centered around zero. ...
edger deseq2 written 3.1 years ago by tonja.r40

Latest awards to tonja.r

Great Question 2.3 years ago, created a question with more than 5,000 views. For FDR and padj in deseq and edger
Epic Question 2.3 years ago, created a question with more than 10,000 views. For FDR and padj in deseq and edger
Great Question 2.3 years ago, created a question with more than 5,000 views. For gene dispersion, what does it mean?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For gene dispersion, what does it mean?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For RUVseq using RUVg most non-differential expressed genes
Popular Question 2.3 years ago, created a question with more than 1,000 views. For RUVseq PCA on raw data, whereas DESeq suggests stabilization
Popular Question 2.3 years ago, created a question with more than 1,000 views. For deseq2 dispersion esimation fit type changed only when computing vst
Popular Question 2.3 years ago, created a question with more than 1,000 views. For fold change calculation in edger
Popular Question 2.3 years ago, created a question with more than 1,000 views. For FDR and padj in deseq and edger
Popular Question 2.3 years ago, created a question with more than 1,000 views. For PCA from deseq and r function differ
Popular Question 2.3 years ago, created a question with more than 1,000 views. For gviz: name of tracks disappeas
Popular Question 2.3 years ago, created a question with more than 1,000 views. For DESeq2 MA plot of encode data
Popular Question 2.9 years ago, created a question with more than 1,000 views. For FDR and padj in deseq and edger
Popular Question 2.9 years ago, created a question with more than 1,000 views. For edger, trended or common dispersion

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