User: bioinfonerd

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bioinfonerd10
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Posts by bioinfonerd

<prev • 12 results • page 1 of 2 • next >
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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 4 weeks ago by bioinfonerd10
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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 7 weeks ago by bioinfonerd10
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Comment: C: Delta z score between control and treatment
... Thanks very much! That's helpful. ...
written 8 weeks ago by bioinfonerd10
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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 8 weeks ago by bioinfonerd10 • updated 8 weeks ago by prakash480
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Comment: C: DESEQ2 application on control vs treatment
... Thanks!! I have corrected it. ...
written 8 weeks ago by bioinfonerd10
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Comment: C: DESEQ2 application on control vs treatment
... Thanks very much!!!!! ...
written 8 weeks ago by bioinfonerd10
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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 8 weeks ago by bioinfonerd10
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Comment: C: Global Median Normalization
... Thanks Kevin, that's really helpful! ...
written 9 weeks ago by bioinfonerd10
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Comment: C: Normalization of gene expression data
... Thanks that was really helpful! ...
written 10 weeks ago by bioinfonerd10
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Global Median Normalization
... Hi everyone, I am new to the normalization techniques and would like to know what is Global median normalization and the steps to apply it on Nanostring gene expression dataset. Thanks!! ...
normalization nanostring written 10 weeks ago by bioinfonerd10 • updated 10 weeks ago by Kevin Blighe28k

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