User: vrehaman

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vrehaman0
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Posts by vrehaman

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Comment: C: DESEQ2 design with multiple conditions
... Dear Michael, Thanks a lot for your quick response and suggestions on multiple covariates. And I have checked the vignette , and will put condition at the end of formula like below. dds <- DESeqDataSetFromMatrix(countData = cts1,colData = coldata,design = ~  batch + age + condition) Thanks &a ...
written 3 months ago by vrehaman0
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DESEQ2 design with multiple conditions
... Dear team, I am working on RNASeq data with batches and later on I have to more covariates to design. I  had tried automating R script but it's not working. How can I automate design part of DESeq2 workflow? My coldata file looks like below condition batch ctrl 1 ...
deseq2 design matrix written 3 months ago by vrehaman0 • updated 3 months ago by Michael Love19k
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Comment: C: Run tweeDEseq on Flux-capacitor RPKM values
... Dear Robert, Thanks a lot for your confirmation and we will surely try the other suggested methods. Right now, we are using HTSeq for getting raw counts and using the same as input to tweeDeSeq. It is performing well. Thanks & Regards Fazulur Rehaman ...
written 6 months ago by vrehaman0
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Run tweeDEseq on Flux-capacitor RPKM values
... Dear Team, For Differential expression, we are using tweeDEseq method which will take read counts as input and normalize counts using TMM method and perform pair wise comparisons. I have used Flux-capacitor for quantifying transcripts which gives read counts and RPKM values as output. here is the ...
tweedeseq differential expression written 6 months ago by vrehaman0 • updated 6 months ago by Robert Castelo2.2k

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