User: Raymond

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Raymond0
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Posts by Raymond

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PCA plot of variance stabilized transformation of normalized counts in limma
... Hi,     I used to plot PCA  using DESeq2, and it works great.  In DESeq2, the normalized counts are transformed through vst(variance stabilized transformation, based on the NB variance ~ expectation relationships?) function, rather than the direct log transformed counts.     I tried limma-voom in ...
edger deseq2 limma-voom written 10 hours ago by Raymond0 • updated 3 hours ago by Steve Lianoglou12k
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Comment: C: DESeq2 got stuck for one night, restarting?
... My design Matrix is design = ~ batch+genotype+sex+condition where batch has 9 level, genotype has 6 levels, sex has 2 levels, and condition has 4 levels. I do not include the PMI information here, where is a continuous number.  I will try limma-voom then. Thanks, Micheal! ...
written 13 days ago by Raymond0
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DESeq2 got stuck for one night, restarting?
... Hi,    My DESeq2 running was stucked for one night, it is normal?  My dataset contains 635 human samples, this is abnormally large: head(ddsTxi) class: DESeqDataSet dim: 6 635 metadata(1): version assays(2): counts avgTxLength dds <- DESeq(ddsTxi) estimating size factors   Note: levels of fac ...
rnaseq deseq2 written 13 days ago by Raymond0 • updated 13 days ago by Michael Love19k
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Comment: C: Simultaneously adding two different covariates in the model gives error in DESeq
... I met with the same problems, trying to model RIN and PMI into my model. It seems that some people would regress these factors (using Combat for example) before doing a DEG analysis. But there are also paper mention that the best way is to model all factors into the design matrix and do DEG analysis ...
written 14 days ago by Raymond0
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DESeq2 with too many rejections
... Hi,   I had a groups of samples with 12 different conditions. I followed the DESeq2 tutorial in Bioconductor, and then plot the rejections:   {plot(metadata(res)$filterNumRej, type="b", ylab="number of rejections", xlab="quantiles of filter") lines(metadata(res)$lo.fit, col="red") abl ...
deseq2 written 11 weeks ago by Raymond0 • updated 11 weeks ago by Michael Love19k
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Analyzing a subgroups of samples, which result should I trust
... Dear friends, I had 6(A,B,C,D,E,F) groups of animals, each containing 7 samples. I run DESeq and compared the DEGs between every two groups. Later, I found group F is biologically far away from other groups (all 6 groups were in the same batch). So, I run DESeq again, and drop the idx in group F. I ...
deseq2 rna-seq written 5 months ago by Raymond0 • updated 5 months ago by funnyjokes1.com0
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Comment: C: Re-calculate DESeq from dds based on another design
... Thanks, Michael. ...
written 7 months ago by Raymond0
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Re-calculate DESeq from dds based on another design
... Hi,     I imported my data from tximport and run the following: ddsTxi_all2 <- DESeqDataSetFromTximport(txi.kallisto_gene, colData = s2c, design = ~ summary) dds2 <- DESeq(ddsTxi2) Later, I saved 'dds2' to my local disk ...
deseq2 written 7 months ago by Raymond0 • updated 7 months ago by Michael Love19k
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Comment: C: To analyze the overall variance, which one to choose, vst or DESeq2 normalized c
... Thanks so much, Michael!  For 'across genes', do you mean the variances of genes in the same group?  I want to compare the variances of the same genes between different groups. In this case, dose vst also help? ...
written 7 months ago by Raymond0
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To analyze the overall variance, which one to choose, vst or DESeq2 normalized counts?
... Hi, All,     I have two groups of RNAseq data, each group have 5 samples. I suspected that drug treatment would increase the overall expression variances in some pathways. So, I planned to compare all gene expression variances in that pathway or even in the top 500 expressed genes. I could calculat ...
deseq2 written 7 months ago by Raymond0 • updated 7 months ago by Alan0

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