User: tonja.r
tonja.r • 40
- Reputation:
- 40
- Status:
- New User
- Location:
- United Kingdom
- Last seen:
- 2 years, 7 months ago
- Joined:
- 4 years, 2 months ago
- Email:
- t*********@googlemail.com
Posts by tonja.r
<prev
• 60 results •
page 1 of 6 •
next >
1
vote
2
answers
935
views
2
answers
... 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 ...
0
votes
1
answer
2.0k
views
1
answers
Comment:
C: DESeq2 MA plot of encode data
... I edited my question with new plots and edgeR results.
...
written 3.4 years ago by
tonja.r • 40
0
votes
1
answer
532
views
1
answer
... 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 3.4 years ago by
tonja.r • 40
• updated
3.4 years ago by
Michael Love ♦ 24k
0
votes
1
answer
2.0k
views
1
answers
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 3.4 years ago by
tonja.r • 40
0
votes
1
answer
2.0k
views
1
answers
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 3.4 years ago by
tonja.r • 40
4
votes
1
answer
2.0k
views
1
answer
... 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 3.4 years ago by
tonja.r • 40
0
votes
1
answer
716
views
1
answers
... 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 3.4 years ago by
tonja.r • 40
0
votes
1
answer
716
views
1
answers
... edited my question
...
written 3.4 years ago by
tonja.r • 40
3
votes
1
answer
716
views
1
answer
... 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 3.4 years ago by
tonja.r • 40
2
votes
1
answer
644
views
1
answer
... 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 3.4 years ago by
tonja.r • 40
Latest awards to tonja.r
Great Question
2.6 years ago,
created a question with more than 5,000 views.
For FDR and padj in deseq and edger
Epic Question
2.6 years ago,
created a question with more than 10,000 views.
For FDR and padj in deseq and edger
Great Question
2.6 years ago,
created a question with more than 5,000 views.
For gene dispersion, what does it mean?
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For gene dispersion, what does it mean?
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For RUVseq using RUVg most non-differential expressed genes
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For RUVseq PCA on raw data, whereas DESeq suggests stabilization
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For deseq2 dispersion esimation fit type changed only when computing vst
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For fold change calculation in edger
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For FDR and padj in deseq and edger
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For PCA from deseq and r function differ
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For gviz: name of tracks disappeas
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For DESeq2 MA plot of encode data
Popular Question
3.3 years ago,
created a question with more than 1,000 views.
For FDR and padj in deseq and edger
Popular Question
3.3 years ago,
created a question with more than 1,000 views.
For edger, trended or common dispersion
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 16.09
Traffic: 321 users visited in the last hour