User: qxiong1
qxiong1 • 0
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Posts by qxiong1
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... I am trying to run GISTIC2 using segment results from Sequenza, but not sure what is the minimum sample size for running GISTIC2? ...
written 14 months ago by
qxiong1 • 0
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... 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" ...
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... 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 15 months ago by
qxiong1 • 0
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... 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 15 months ago by
qxiong1 • 0
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... vst() works well, Kevin, thank you very much for your help! ...
written 16 months ago by
qxiong1 • 0
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... 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 16 months ago by
qxiong1 • 0
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... 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 ...
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