User: Nicola

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Nicola0
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Posts by Nicola

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Comment: C: Turn off the functions of estimating dispersions and gene-wise dispersion estima
... Thank you for your kind answer,Micheal last question, would transformed counts fit negative binomial distribution? ...
written 5 weeks ago by Nicola0
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Comment: C: Turn off the functions of estimating dispersions and gene-wise dispersion estima
... If I run this code, how would I modify it better? idx1<-which(rowMeans(Countset)>1) CountSet2<-Countset[idx1,] counts.spikein = as.matrix(CountSet2, colnames = FALSE, row.names = FALSE) ddsHTSeq1<- DESeqDataSetFromMatrix(counts.spikein, colData, design =~batch+condition) dds<-esti ...
written 5 weeks ago by Nicola0
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Comment: C: Turn off the functions of estimating dispersions and gene-wise dispersion estima
... Why could't remove batch from (normalized) counts ? And what's a better manner to get the normalized data without batch effect? ...
written 5 weeks ago by Nicola0
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Comment: C: Turn off the functions of estimating dispersions and gene-wise dispersion estima
... Thank you! Micheal ! I know I can call the sub functions size factor estimation,But the sub functions size factor estimation can't remove the batch effect ...
written 5 weeks ago by Nicola0
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Turn off the functions of estimating dispersions and gene-wise dispersion estimates
... I have RNA-Seq data from two batches and know there is significant batch effect in the data.And I just want to get the normalized data without batch effect,and the data still fits a negative binomial distribution. I run code like this : > counts.spikein = as.matrix(CountSet2, colnames = FALSE, ...
deseq2 written 5 weeks ago by Nicola0 • updated 5 weeks ago by Michael Love23k
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Comment: C: DESeq2: RNA-Seq time series analysis after removal of batch effect
... Thanks a lot for your kind help! ...
written 3 months ago by Nicola0
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DESeq2: RNA-Seq time series analysis after removal of batch effect
... Hi, I'm trying to use DESeq2 to perform time series analysis like a one-way ANOVA on multi-groups of samples,but there is a obvious batch effect in my data . I would like to generate a single p-value that indicates difference among the time without batch effect. and this is my coldata: - List ...
deseq2 time series remove batch effect written 3 months ago by Nicola0
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Comment: C: deseq2 remove batch effect and one-way anova at one time
... > dds <- DESeqDataSetFromMatrix(countData = Data, colData, design= ~batch+condition) > dds = DESeq(dds, test = "LRT", reduced = ~ 1+batch) estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model a ...
written 3 months ago by Nicola0

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