## User: serpalma.v

serpalma.v40
Reputation:
40
Status:
New User
Location:
Germany
Last seen:
3 months, 2 weeks ago
Joined:
3 years, 10 months ago
Email:
s*********@gmail.com

#### Posts by serpalma.v

<prev • 34 results • page 1 of 4 • next >
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... Hello! I am using SNPRelate to calculate Fst for sliding windows. There are two things that I cannot find information about. (1) If I pass a set of samples having a specific order, for example and their corresponding populations: > samps [1] "H07750-L1" "H07754-L1" "H07760-L1" "H07775 ...
written 3 months ago by serpalma.v40 • updated 3 months ago by zhengx30
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... Hello, in the vignette for SNPRelate, under PCA, the plot is labeled as x="eigenvector 2" and y="eigenvector 1". My knowloedge on PCA is very basic and I was wondering if this is the same as x="PC2" and y="PC1". Similarly, I want to also ask if the element \$eigenvect in the pca object ...
written 5 months ago by serpalma.v40 • updated 4 months ago by Stephanie M. Gogarten670
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... If I run DESeq(betaPrior=FALSE) I get two coefficients: the intercept (group A) and the difference between condition B versus A. dds <- makeExampleDESeqDataSet() res1 <- DESeq(dds, betaPrior = FALSE) resultsNames(res1) [1] "Intercept" "condition_B_vs_A" If I run DESeq(betaPrior=TRU ...
written 17 months ago by serpalma.v40 • updated 17 months ago by Michael Love24k
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... I plotted the shrinked fold changes against the mean and the extreme gene is now shown significant but almost not-regulated (please see figure in link). Sorry but I did not get the part of subsetting after lfc shrinking by abs(log2FoldChange) > 0.5. Did you mean to remove the subset having large ...
written 17 months ago by serpalma.v40
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... Hi Michael, the version is DESeq2_1.18.1 I did the changes you mentioned and LFC shrinkage worked. Thanks again!   ...
written 17 months ago by serpalma.v40
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... Trying to run lfcShrink for the coefficient cond2 vs cond1, using lfcShrink(dds2, coef=4) (first 3 coefficients are for the countries) gives "Error: subscript contains invalid names". I tried changing the coef variable to the name of the coefficient, and also using the contrast argument with both, t ...
written 17 months ago by serpalma.v40
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... Hello I used DESeq2 to perform differential expression between three groups (condition1, condition2 and condition3). Samples also come from three different countries. PCA (using rlog transformed data) showed a similar pattern of clustering using country and condition (please see link) So I controll ...
written 17 months ago by serpalma.v40 • updated 17 months ago by Michael Love24k
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... Dear community, I am analyzing RNAseq data set with DESeq2. Samples are grouped in three groups: one control group (n=16) and two case groups (case 1 and 2, n=6 and n=8, respectively). I want to find differentially expressed genes of both case groups against the control group, but also against eac ...
written 19 months ago by serpalma.v40 • updated 19 months ago by Michael Love24k
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... The response says: If you control the FDR at a given level for each of 5 contrasts separately, then you have automatically controlled the FDR at the same level for all 5 contrasts together. I think is contradictory to what is writen in the DESeq2 Vignette (text cited in the initial post).  ...
written 20 months ago by serpalma.v40 • updated 20 months ago by Michael Love24k
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... I have a data set where samples are grouped according to their health status (3 levels) and sampling timepoints (2 levels for each sample). This would be a simplified version of the data set: df <- data.frame(status = c( rep("healthy", 4), rep("condition1", 4), rep("condition2", 4) ), ...
written 20 months ago by serpalma.v40 • updated 20 months ago by James W. MacDonald50k

#### Latest awards to serpalma.v

Popular Question 17 months ago, created a question with more than 1,000 views. For matching probes to genes from pd.porgene.1.1.st array
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Model matrix for anova in limma
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Does limma calculate pvalues using log2 fold changes or with linear values?
Scholar 3.6 years ago, created an answer that has been accepted. For A: Model matrix for anova in limma

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