User: yifangt

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yifangt10
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Posts by yifangt

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Count matrix from Kallisto as input for DESeq2
... Thanks Michael! I meant my situation is as "I only have gene name in the abundance file(no transcript ID)" too. The reference is a uncommon organism and the genome sequence is from de novo assembly and genes/CDS are from prediction. So that I do not have every transcript for each gene.   ...
written 3 days ago by yifangt10
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Comment: C: Count matrix from Kallisto as input for DESeq2
... Hi Michael, I just came across this scenario you asked that my reference only contains CDS from computational annotation. It seems there are many information missing by this reference. Can I ask for your advice on the kallisto est_counts as the transcripts level only? Thanks! ...
written 6 days ago by yifangt10
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Comment: C: SummarizedExperiment Error! expressionSet data structure
... Thanks a lot! ...
written 16 months ago by yifangt10
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Comment: C: SummarizedExperiment Error! expressionSet data structure
... I think you are right that the problem is the "data.frame" of the count table.  After I change this line to create the ExpressionSet object: barley.eset <- new("ExpressionSet", assayData=assayDataNew(exprs=as.matrix(barleydata)), phenoData=pData,featureData=fData) and SummarizedExperiment(expr ...
written 16 months ago by yifangt10
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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 16 months ago by yifangt10
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Answer: A: SummarizedExperiment Error! expressionSet data structure
... Added to original post   ...
written 16 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 16 months ago by yifangt10 • updated 16 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 18 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 18 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 18 months ago by yifangt10

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