User: bioinfonerd

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bioinfonerd30
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Posts by bioinfonerd

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Comment: C: DESEQ2 control vs multiple treatment
... Thanks a lot! It works ...
written 4 months ago by bioinfonerd30
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DESEQ2 control vs multiple treatment
... Hi I have four arms of a study with 50 matched patient samples data for all Arms 1,2,3 and 4 where Arm1: Control Arm2: Drug1 Arm3: Drug2 Arm4: Drug3 How can I compare Arm2,3 and 4 with Arm1 individually performing a DESeq. Could you please help me with the DESeq design? Thanks! ...
rna-seq written 4 months ago by bioinfonerd30
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Whole Exome Sequencing Depth
... Hi, I want to calculate Copy number variations(CNV) from Whole exome seq data. What is the correct sequencing depth that can result in correct identification of CNVs. Also is it possible to extract somatic CNVs without matched tumor normal? Thanks. ...
cnv written 4 months ago by bioinfonerd30
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DESeq2 log2 fold change
... Hi everyone, I did the DESeq2 on my Nanostring gene expression data using the below code: dds <- DESeqDataSetFromMatrix(countData = counts_set,colData = annotation,design = ~ pt_id+treatment) sizeFactors(dds) <- estimateSizeFactorsForMatrix(counts(dds)) dds <- DESeq(dds) ...
deseq2 nanostring written 5 months ago by bioinfonerd30
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Change in variance Treated-Vehicle
... Hi everyone, I have gene expression data for 10 control and 10 treatment samples. For a particular gene I need to find the change between control and treatment and following are the steps that I think to do: 1. Log2 transform 2. Z-score calculation for control and treated together 3. Standard devi ...
rna-seq written 6 months ago by bioinfonerd30
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Comment: C: Delta z score between control and treatment
... Thanks very much! That's helpful. ...
written 6 months ago by bioinfonerd30
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Delta z score between control and treatment
... Hi everyone, I have RNA expression data for 20 control and 20 matched treatment samples. I need to plot z-score change for a gene signature between control and treatment for all the 20. This is what I think to do: 1. Log2 of the expression values 2. Calculate z-scores separately for all control 3 ...
rna-seq written 6 months ago by bioinfonerd30 • updated 6 months ago by Prakash730
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Comment: C: DESEQ2 application on control vs treatment
... Thanks!! I have corrected it. ...
written 6 months ago by bioinfonerd30
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Comment: C: DESEQ2 application on control vs treatment
... Thanks very much!!!!! ...
written 6 months ago by bioinfonerd30
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DESEQ2 application on control vs treatment
... `enter code here`Hi everyone, I have 5 control samples and 5 treatment samples for the same patients and I would like to extract the differentially expressed genes between control and treatment samples. The method I am using now is: dds <- DESeqDataSetFromMatrix(countData = counts_set,col ...
deseq nanostring written 6 months ago by bioinfonerd30

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