User: tonja.r
tonja.r • 40
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Posts by tonja.r
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... 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 ...
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C: DESeq2 MA plot of encode data
... I edited my question with new plots and edgeR results.
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written 3.2 years ago by
tonja.r • 40
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... 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 ...
written 3.2 years ago by
tonja.r • 40
• updated
3.2 years ago by
Michael Love ♦ 23k
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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 3.2 years ago by
tonja.r • 40
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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 3.2 years ago by
tonja.r • 40
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... 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 ...
written 3.2 years ago by
tonja.r • 40
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674
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... 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?
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written 3.3 years ago by
tonja.r • 40
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674
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... edited my question
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written 3.3 years ago by
tonja.r • 40
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674
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... 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 ...
written 3.3 years ago by
tonja.r • 40
2
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616
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... 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.
...
written 3.3 years ago by
tonja.r • 40
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