User: Biologist

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Biologist70
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Posts by Biologist

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Comment: C: EdgeR for differential analysis between two cell lines without replication
... Thank you very much for the reply. ...
written 3 months ago by Biologist70
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Comment: C: EdgeR error for differential analysis between two cell lines
... Hi Gordon, Thank you. I followed the tutorial and did the analysis. I have raw counts data of 72 genes for two cell-lines in dataframe "df". Three columns. First columns has genes and other columns are cell-lines. df <- data.frame(df[,-1], row.names=df[,1]) library(edgeR) y <- DGEList(cou ...
written 3 months ago by Biologist70
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Comment: C: EdgeR error for differential analysis between two cell lines
... Hi Michael, I would like to know whether I can do differential analysis between two cell-lines with Deseq2? ...
written 3 months ago by Biologist70
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EdgeR for differential analysis between two cell lines without replication
... I have data like following: 56318 genes and two cell-lines with counts data. head(counts)[1:5,] Name Description Cell-line1 Cell-line2 1 ENSG00000223972 DDX11L1 1 2 2 ENSG00000227232 WASH7P 1639 1138 3 ENSG00000243485 MI ...
rnaseq edger differential gene expression written 3 months ago by Biologist70 • updated 3 months ago by Gordon Smyth35k
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Comment: C: Does Fold change cutoff changes the FDR value using glmTreat function in edgeR?
... This is very helpful. Thank you for the answer. ...
written 4 months ago by Biologist70
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Comment: C: Does Fold change cutoff changes the FDR value using glmTreat function in edgeR?
... yes, I gave the code and made necessary changes in my question. ...
written 4 months ago by Biologist70
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Does Fold change cutoff changes the FDR value using glmTreat function in edgeR?
... I'm doing differential analysis between two groups A & B With Fold change > 2 and FDR < 0.05 I have got more than 600 differentially expressed genes. Among them I see the following gene. tr <- glmTreat(fit, contrast=contrast.matrix, lfc=log2(2)) tab2 <- topTags(tr,n=Inf, adjust.me ...
edger R bioconductor fdr diffferential expression written 4 months ago by Biologist70 • updated 4 months ago by James W. MacDonald48k
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Comment: C: Why DESeq2 and edgeR give different results?
... Hi Michael, I have a very small cohort 28 cancer vs 3 Normal only. For this type of cohort for differential analysis do I need keep any special arguments while using deseq2? ...
written 4 months ago by Biologist70
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Comment: C: Why DESeq2 and edgeR give different results?
... Thank you very much ...
written 5 months ago by Biologist70
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Why DESeq2 and edgeR give different results?
... Dear All, I have a matrix "U2" with 44 samples (41 Disease + 3 Normal) as columns and approx. 15k genes as rows. "coldata" is where samples as rows and columns "Subtypes" and  "Type". Column "Type" is with Disease and Normal. library(DESeq2) dds <- DESeqDataSetFromMatrix(countData = U2, colDat ...
rnaseq edger deseq2 differential gene expression written 5 months ago by Biologist70 • updated 4 months ago by Gordon Smyth35k

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