User: newbie

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newbie30
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Posts by newbie

<prev • 19 results • page 1 of 2 • next >
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Comment: C: what to do when differential analysis heatmap looks like this?
... Thanks for the answer. Have a similar doubt. What answer I can give if the DEA heatmap looks like above, where 9 samples of subtype A are away from the main cluster? ...
written 2 days ago by newbie30
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what to do when differential analysis heatmap looks like this?
... Hello, I'm working with rnaseq data of breast cancer samples. There are a total of 40 samples. Among 40 samples, 26 samples are of subtype A and 14 are subtype B. I did differential analysis with samples between Subtype A and Subtype B with edgeR. Differentially expressed genes are based on FDR &l ...
R differentialanalysis rna-seq edger heatmap written 2 days ago by newbie30 • updated 3 hours ago by eric.audemard0
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Comment: C: Differential analysis using cell-line data with replicate information
... @ATpoint Could you please tell me what is wrong in my above code ...
written 23 days ago by newbie30
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Comment: C: Differential analysis using cell-line data with replicate information
... Instead of showing in table, I'm showing the counts data for all samples with some genes. data <- structure(list(Cell1_foxcut12 = c(4L, 8L, 3L, 4L, 7318L, 25317L, 41L, 0L, 0L, 0L), Cell2_foxcut11 = c(9L, 11L, 2L, 6L, 4959L, 2621L, 38L, 0L, 0L, 0L), Cell1_foxcut11 = c(0L, 3L, 2L, 0 ...
written 23 days ago by newbie30
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Comment: C: Differential analysis using cell-line data with replicate information
... May I know how this can be done please. I haven't seen anywhere about this type of analysis, so I'm not at all aware about how to do this. ...
written 23 days ago by newbie30
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Comment: C: Differential analysis using cell-line data with replicate information
... @ATpoint Hi, could you please tell me how to create design matrix for the differential analysis within the same cell-line Do you think the below code is right? library(edgeR) group <- factor(paste0(coldata$TYPE)) y <- DGEList(data,group = group) y$samples ## Filteri ...
written 23 days ago by newbie30
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Comment: C: Differential analysis using cell-line data with replicate information
... Yes, differential analysis needs to be done within the same cell-line. I edited my question. Could you please tell me how to give the syntax for group, design matrix and contrasts using edgeR? thanq ...
written 24 days ago by newbie30
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Comment: C: Differential analysis using cell-line data with replicate information
... Sorry, my mistake. It should be something like this Cell1_foxcut samples vs Cell1_HA samples Cell2_foxcut samples vs Cell2_HA samples ...
written 24 days ago by newbie30
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Comment: C: Differential analysis using cell-line data with replicate information
... Please check this: ### Differential Analysis library(edgeR) group <- factor(paste0(coldata$Type)) y <- DGEList(data,group = group) y$samples ## Filtering (Based on smallest number of samples among two groups do the filtering) keep <- rowSums(cpm(y) > 0. ...
written 24 days ago by newbie30
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Differential analysis using cell-line data with replicate information
... I have a total of 8 samples, 4 controls and 4 Foxcut gene over expressed samples. The column data for all the 8 samples look like below with replicate and cell-line information: Samples TYPE Replicate Cell-lines Cell1_HA1 Control 1 1 ...
R celllines differentialanalysis rna-seq edger written 24 days ago by newbie30

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