User: vrehaman

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vrehaman0
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Posts by vrehaman

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Comment: C: DESEQ2 normalize data of population data
... Dear Michael, I have one more question. Since, we have only one comparsion which is diseased relative to Normal, Is there any possibility, I might know the family belongs to upregulated or down regulated genes.  Please let me know. Thanks & Regards Fazulur Rehaman ...
written 12 days ago by vrehaman0
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Comment: C: DESEQ2 normalize data of population data
... Dear Michael, Thanks a lot for your confirmation and suggestions on factor levels. Thanks & Regards Fazulur Rehaman ...
written 13 days ago by vrehaman0
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Comment: C: DESEQ2 normalize data of population data
... Dear Michael, Thanks a lot for your suggestions. At first, I used the same model ~family + condition  Here are the details: which will control for family baseline, while finding genes where the diseased samples show DE relative to normal. It means only one comparison where we can find genes dis ...
written 14 days ago by vrehaman0
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Comment: C: DESEQ2 normalize data of population data
... Dear Michael, Thanks a lot for your quick response. Please find below the details What kind of genes are you looking for? Genes commonly DE in diseased relative to normal? We are looking for more diabetic and obesity genes commonly DE in diseased relative to normal. You cannot perform DE within ...
written 14 days ago by vrehaman0
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DESEQ2 normalize data of population data
... Dear Team, I want to perform differential expression on counts generated from featureCounts. Each family has different disease. Can we perfrom differential expression across all samples? or since disease is different from family to family, should we perform separately family by family? Example sam ...
deseq2 multiple factor design written 15 days ago by vrehaman0 • updated 15 days ago by Michael Love19k
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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 6 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 6 months ago by vrehaman0 • updated 6 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 8 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 8 months ago by vrehaman0 • updated 8 months ago by Robert Castelo2.2k

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