User: Maryam

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Maryam0
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Posts by Maryam

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Deseq normalization with adjusting gene length
... Here is the R code for whoever needs it. cts <- as.matrix(read.csv("Count_data.txt", row.names = 1, header= TRUE, sep="\t")) coldata <- read.csv("coldata.txt", row.names = 1, sep="\t") dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition) txdb <- make ...
written 5 months ago by Maryam0
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Comment: C: Deseq normalization with adjusting gene length
... So many thanks ...
written 5 months ago by Maryam0
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Comment: C: Deseq normalization with adjusting gene length
... Thanks Michael, but I do not want FPKM. I need deseq2 normalization which accounts gene length in normalization too. Is it possible? ...
written 5 months ago by Maryam0
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Deseq normalization with adjusting gene length
... Hi all, I asked the question in Biostar and then I got the answer that I should use deseq2 normalization with gene length adjustment. Is it possible to use deseq2 normalization with gene length adjustment like as FPKM gene length adjustment? I have 250 samples from healthy and disease states and I w ...
normalization deseq2 written 5 months ago by Maryam0
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Comment: C: Using deseq2 with batch effects and classification as downstream analysis
... Many thanks ...
written 7 months ago by Maryam0
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Using deseq2 with batch effects and classification as downstream analysis
... I'm using Deseq2 for differential gene expression analysis and then for downstream analysis i'm going to classify healthy vs disease states using support vector machine. The data comprises of healthy and disease states which sequenced in 13 batches. I have 2 questions: 1) I used design = ~ batch + ...
classification deseq2 batch effect written 7 months ago by Maryam0 • updated 7 months ago by Michael Love23k

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