User: hamsasekar02

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Posts by hamsasekar02

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DESeq2 correct pairwise comparisions
... I have resultNames(dds) as -: Model - > dds <- DESeqDataSetFromMatrix( + countData = countTable, + colData = colTable, design = ~ condition+time+condition:time) > dds_lrt_time <- DESeq(dds, test="LRT", reduced = ~ condition + time) > resultsNames(dds_lrt_time) [1] "Intercept" ...
rna-seq written 20 days ago by hamsasekar020
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Comment: C: DESeq2 model design
... *On the contrary, if they didn't have the T_0 sample, their mock-infection placebo could have profound time-dependent effects but they'd have no baseline sample against which to compare those effects and wouldn't be able to identify them* This is exactly what we want to know and we have two genotype ...
written 23 days ago by hamsasekar020
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Comment: C: DESeq2 model design
... yes , we are also taking it as the baseline to compare with mock and infected ...
written 25 days ago by hamsasekar020
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Comment: C: DESeq2 model design
... Thank you for the quick reply We need to actually compare uninfected with mock and infected, so merging will be a little difficult option ...
written 25 days ago by hamsasekar020
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Comment: C: DESeq2 model design
... Thank you for the reply Sorry, I forgot to write the point that i have 3 biological replicates for each . I want to compare uninfected with mock and with infected according to my work plan. ...
written 25 days ago by hamsasekar020
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DESeq2 model design
... I have a data , like this Genotype condition time A uninfected 0day A uninfected 0 day A uninfected 0 day A mock 2day A mo ...
rna-seq written 25 days ago by hamsasekar020 • updated 25 days ago by russhh4.3k
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Comment: C: DESeq2 result contrast
... Thank you Sir, I understood that ("GenotypeII.condition infetced") will give me difference in in mock vs infected samples of GenotypeII taking care of mock vs infected levels in the reference genotype (Genotype I) . Is my understanding correct ?? ...
written 28 days ago by hamsasekar020
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Comment: C: DESeq2 result contrast
... Thank you Sir for the reply To make it more clear, I want to compare Genotype II vs Genotype I in infected vs mock condition, and also seeing the condition effect of GenotypeII with respect to Genotype I ...
written 29 days ago by hamsasekar020
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DESeq2 result contrast
... I have three genotypes (I,II,III) and conditions (infected,mock) When i do the DESeq2 analysis with model `Genotype+condition+Genotype:condition` I get the following result [1] "Intercept" "Genotype_II_vs_I" [3] "Genotype_III_vs_I" "condition_i ...
R written 29 days ago by hamsasekar020 • updated 29 days ago by ATpoint15k

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