User: Raymond

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Raymond0
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Posts by Raymond

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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 20 days ago by Raymond0 • updated 20 days 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 3 months ago by Raymond0 • updated 3 months ago by funnyjokes1.com0
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Comment: C: Re-calculate DESeq from dds based on another design
... Thanks, Michael. ...
written 5 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 5 months ago by Raymond0 • updated 5 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 5 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 5 months ago by Raymond0 • updated 5 months ago by Alan0
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Comment: C: How to get the latest KEGG pathway
... Thanks for the information, Smyth.  ...
written 6 months ago by Raymond0
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How to get the latest KEGG pathway
... Hi,      I want to draw KEGG pathways with my nodes colored correlated to p-value*log(foldchange). From : http://keggscape.readthedocs.io/en/latest/pythonscripting.html I used "http://rest.kegg.jp/list/pathway/hsa" to get all human kegg pathways, and "http://rest.kegg.jp/get/' + pathwayid + '/kg ...
kegggraph kegg kegg.db written 6 months ago by Raymond0
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Comment: C: what the first row without a gene name?
... Thanks Michael.  I tried the first way, giving them the paste0("UNKNOWN",transcriptID) as the gene ID.  ...
written 6 months ago by Raymond0
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what the first row without a gene name?
... Hi, all,       I aligned my RNAseq raw data to cDNA using Kallisto and import the result using tximport as suggested by the DESeq2 tutorial (tx2gene maps ensembl_transcript_id to ext_gene symbol) txi.kallisto_gene <- tximport(files, type = "kallisto", tx2gene=tx2gene,ignoreTxVersion=TRUE) Whe ...
deseq2 written 6 months ago by Raymond0 • updated 6 months ago by Michael Love19k

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