User: yifangt

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yifangt10
Reputation:
10
Status:
New User
Location:
Canada/NRC
Last seen:
2 days, 19 hours ago
Joined:
1 year, 9 months ago
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y******@gmail.com

Posts by yifangt

<prev • 18 results • page 2 of 2 • next >
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Comment: C: SummarizedExperiment Error! expressionSet data structure
... Thanks Martin! Here is my script to create barley.est: > library(Biobase); library(GenomicRanges) > library(SummarizedExperiment) > barleydata <- read.table("../20160323_rerun/results/all_featureCounts_by_gene.txt") $ head all_featureCounts_by_gene.txt #This was done under OS conso ...
written 19 months ago by yifangt10
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Answer: A: SummarizedExperiment Error! expressionSet data structure
... Added to original post   ...
written 19 months ago by yifangt10
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SummarizedExperiment Error! expressionSet data structure
... Hello, I was trying RNAseq pipeline following this link. I had no problem with the sample data hammer, but not with my own. This is the error message: se <- SummarizedExperiment(exprs(barley.eset)) Error in if (is.null(nms) && 0L != ncol(assays[[1]])) stop("'SummarizedExperiment' as ...
software error summarizedexperiment written 19 months ago by yifangt10 • updated 19 months ago by Martin Morgan ♦♦ 20k
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Comment: C: DESeq2 RNAseq analysis with "matrix not full rank" error corrected.
... So I am doing the analysis separately for each variety to compare the treated vs control: > coldata.Be <- data.frame(row.names = c("BeC-1","BeC-2","BeT-1","BeT-2"), treatment = rep(c("control","treated"),each = 2)) > coldata.Be treatment BeC-1 control BeC-2 control BeT-1 treat ...
written 21 months ago by yifangt10
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Comment: C: DESeq2 RNAseq analysis with "matrix not full rank" error corrected.
... First of all, thanks for the scripts that are what I was looking for! I did not anticipate the discussion on the selection of T and S here, which seems another big topic on experiment design. Selection of T and S is basically the idea of "Biological replicates" which is adopted from microarray/QRT- ...
written 21 months ago by yifangt10
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Answer: A: DESeq2 RNAseq analysis with "matrix not full rank" error corrected.
... Thanks! Several points are in my mind: 1) Test the treatment vs control effect across T and S; 2) Test the treatment vs control effect within T and S, respectively; 3) Test the treatment vs control effect across all varieties (this should NOT be surprising if any significance turns out); 4) Tes ...
written 21 months ago by yifangt10
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Answer: A: DESeq2 RNAseq analysis with "matrix not full rank" error corrected.
... Thanks Michael! My materials are plant/crops. S is susceptible vs T tolerant to stress. These are the 2 groups in trait/phenotype. Varieties can be called "genotypes" here, and they are different lines of the same plant/crop. 1) I am not sure my way to fix the "model matrix is not full rank" error ...
written 21 months ago by yifangt10
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DESeq2 RNAseq analysis with "matrix not full rank" error corrected.
... Hello, I'd like to get some help on my RNAseq data analysis with DESeq2. The experiment is balanced design with multiple factors with biological/technical replicates. > coldata group variety treatment BeC-1 T Be control BeC-2 T Be control BeT-1 T Be t ...
deseq2 multiple factor design written 21 months ago by yifangt10

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