User: Ekarl2

gravatar for Ekarl2
Ekarl250
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50
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New User
Location:
Sweden
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3 years, 5 months ago
Joined:
4 years, 10 months ago
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g********@student.gu.se

Posts by Ekarl2

<prev • 18 results • page 1 of 2 • next >
11
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How does edgeR compare to lme4?
... I am working on an RNA-seq dataset for differential expression: 4 environments, 4 biological replicates per environment. There are also 4 batches, but they are orthogonal to environments, so all environments are equally represented among all batches. I lean towards EdgeR. I find it more user friend ...
edger rna-seq lme4 mixed model random effects written 3.4 years ago by Ekarl250 • updated 3.4 years ago by Gordon Smyth39k
10
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8 follow
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Is Limma's removeBatchEffect() and log2() commutative?
... I am working on an RNA-seq dataset and have been using the EdgeR differential expression analysis methods with GLMs. Here, I have specified batch as a factor in the design matrix. The batch factor is uncorrelated with the other experimental factors and each batch is evenly represented among all envi ...
limma rna-seq removebatcheffect() written 3.6 years ago by Ekarl250 • updated 22 months ago by alakatos110
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EdgeR: Each treatment as a group versus treatment effects over all times?
... From the wonderful edgeR user manual (sections 3.3.1 p. 32 and section 3.3.3 p. 34) we find two different approaches: (1) each treatment is a different group, and tests are done between groups. (2) treatment effects over all times (e. g. either drug conc. 1 or drug conc. 2 versus baseline). The c ...
limma edger written 3.7 years ago by Ekarl250 • updated 3.7 years ago by Aaron Lun25k
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Does order of removeBatchEffect() and DE subsetting matter for clustered heat map visualization?
... I want to make a clustered heat map for the differentially expressed genes I identified with EdgeR where the batch effect was modeled as an experimental factor. To do this, I used the limma package removeBatchEffect() after TMM-normalization and log2 CPM transformation on the DE subset of the raw ex ...
limma edger rna-seq removebatcheffect() batch written 3.7 years ago by Ekarl250 • updated 3.7 years ago by Aaron Lun25k
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Comment: C: EdgeR: is more than one control per batch an issue?
... A quick follow-up. The reason for the fact that batch 1 only has one control is that one of them failed. To compensate, they made another control in batch 4, but that is the only sample in that batch. My instinct is this sample should be excluded because there is only one sample for batch 4, so ther ...
written 3.8 years ago by Ekarl250
4
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671
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EdgeR: is more than one control per batch an issue?
... The current dataset I am looking at has seven environments (control and three different concentrations of exposure A separately and exposure B separately) and each exposure/concentration combination has three replicates (one in each batch). My goal is to compare each of the six experimental conditi ...
edger batch effect written 3.8 years ago by Ekarl250 • updated 3.8 years ago by Aaron Lun25k
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Comment: C: Is this design matrix correct (treament factor with three levels)?
... I have fixed the display problem now; trtB was in column 2, 5 and 8, whereas trtA was in column 3, 6, 9 in the original matrix file. So that order was not alphabetical. How does it look? ...
written 3.8 years ago by Ekarl250
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Comment: C: Is this design matrix correct (treament factor with three levels)?
... Looks like it was a result of me changing the real treatment names to A and B labels too quickly (real name of treatment A is after real name of treatment B alphabetically), so they got switched. Let me fix that right away. ...
written 3.8 years ago by Ekarl250
4
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1
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Is this design matrix correct (treament factor with three levels)?
... I am working with a dataset that has three different treatments (control, A, B). Each sample has only one of these. Each of control, A and B, has three replicates. I want to test for the effect of A on the one hand and the effect of B on the other. Matrix headers: ctrl1 trtB1 trtA1 ctrl2 ...
limma edger design matrix written 3.8 years ago by Ekarl250
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Comment: C: Is the following a correct usage of Limma's removeBatchEffect() for clustered he
... Thank you for your valuable reply, particularly with regards to prior count and rpkm(). If I data <- t(scale(t(logCPM_no_batch), scale=T)) instead of scale=F and set scale="none" in heatmap() would this produce a heat map that had both mean and sd scaled, thus being more in line with what is ...
written 3.9 years ago by Ekarl250

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