User: aangajala

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aangajala0
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Posts by aangajala

<prev • 15 results • page 1 of 2 • next >
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Comment: C: DESEQ2 Grouping vs interaction and dds
... I apologize for this,thanks so much for your time.  ...
written 9 days ago by aangajala0
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Comment: C: DESEQ2 Grouping vs interaction and dds
... You just made my day saying so :) I did a lot of work yesterday with out removing. So, I was worried. ...
written 9 days ago by aangajala0
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Comment: C: DESEQ2 Grouping vs interaction and dds
... What is the difference between , using group and interaction? Is it going to give same results? dds <- DESeqDataSetFromMatrix(countData = cts,                               colData = coldata,                               design = ~ type + ER) dds$group <- factor(paste0(dds$type, dds$ER)) des ...
written 9 days ago by aangajala0
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Comment: C: DESEQ2 Grouping vs interaction and dds
... Thank you. What will happen if I do not remove. Then it will just overwrite the dds, so basically it is new dds right? or does it append the dds , I mean mix with the previous one?  ...
written 9 days ago by aangajala0
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Comment: C: DESEQ2 Grouping vs interaction and dds
... Here is my Coldata, I am trying to verify what I am doing is correct? ...
written 10 days ago by aangajala0
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Comment: C: DESEQ2 Grouping vs interaction and dds
... > head(coldata)                                 sampletype                      race androgen_receptor_statu TCGA.3C.AAAU.01A.11R.A41G.13 Primary Tumor                     white                positive TCGA.3C.AALI.01A.11R.A41G.13 Primary Tumor black or african american                negative TC ...
written 10 days ago by aangajala0
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DESEQ2 Grouping vs interaction and dds
... Question #1: I tried to look the documentation for interaction.But, Unable to understand difference between groups and interaction.So difference between following codes, Is it basically same, different ways of doing it? dds$group <- factor(paste0(dds$race, dds$sampletype)) design(dds) <- ~ g ...
deseq2 written 10 days ago by aangajala0 • updated 9 days ago by Michael Love16k
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Comment: A: DESeq2 using multiple conditions
... Sorry... design(ddsMF) <- formula(~ type + condition) My question is how many variables can we give. Here in this code only two variables are used? Or is there a limit? ...
written 12 days ago by aangajala0 • updated 12 days ago by Michael Love16k
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DESeq2 using multiple conditions
... Hello, I have multiple conditions, such as condition1( Normal and Cancer), condition2( age bellow 50 and above50), so I want to see DEGs of age in Normal samples and cancer. So for this do I have produce dds twice by separating coldata , one for normal and one for primary. And then use condition fo ...
deseq2 written 12 days ago by aangajala0 • updated 12 days ago by Michael Love16k
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Comment: C: Normalization using DESeq
... Okay thank you so much. ...
written 13 months ago by aangajala0

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