User: qxiong1

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qxiong10
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Posts by qxiong1

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How many samples needed for run GISTIC2 to get meaningful results
... I am trying to run GISTIC2 using segment results from Sequenza, but not sure what is the minimum sample size for running GISTIC2? ...
genome next-gen rna-seq sequencing written 2.2 years ago by qxiong10 • updated 8 months ago by Biostar ♦♦ 20
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Use Sequenza output to run GISTIC2
... From Sequenza output, there are following 13 columns, I am wondering which one I should use for GISTIC2 to calculate Set.CN? "chromosome" "start.pos" "end.pos" "Bf" "N.BAF" "sd.BAF" "depth.ratio" "N.ratio" "sd.ratio" "CNt" "A" "B" "LPP" ...
sequencing written 2.2 years ago by qxiong10 • updated 7 months ago by Thind amarinder110
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Comment: C: Can I put FF and FFPE samples together for RNA-seq data analysis
... Hi Kevin, could you please take a look at my code and see if it is correct for the covariate analysis in DESeq? design <- formula(~ Tissue + Response) dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = design) dds <- DESeq(dds) res <- results(dds, contrast=c(" ...
written 2.2 years ago by qxiong10
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Comment: C: Can I put FF and FFPE samples together for RNA-seq data analysis
... Many thanks for your help. One more question: do you know if these rlog or VST transformed counts are normalized counts adjusted for the covariates or non-normalized counts? My main concern is if these transformed counts can be directly used for statistical tests on gene expression difference betwee ...
written 2.3 years ago by qxiong10
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Comment: A: Can I put FF and FFPE samples together for RNA-seq data analysis
... vst() works well, Kevin, thank you very much for your help! ...
written 2.3 years ago by qxiong10
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Comment: C: Can I put FF and FFPE samples together for RNA-seq data analysis
... ATpoint and Kevin. Thanks a lot. I have added a covariate (Tissue) to the design matrix and seems it indeed accounted for the difference between FF and FFPE. However, another issue arises. I want to output the corrected counts using select <- counts(dds,normalized=TRUE), DESeq2 still gave me the ...
written 2.3 years ago by qxiong10
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Can I put FF and FFPE samples together for RNA-seq data analysis
... I have RNA-seq data for both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) samples from prostate cancer. I want to put these two types of data together for data analysis since the sample size will be very small if just using one type. Does anybody know if this is OK? I saw that sever ...
design covariate rna-seq written 2.3 years ago by qxiong10 • updated 2.3 years ago by ATpoint44k

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