User: anpham

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anpham0
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Posts by anpham

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Expression profile from $E from Voom
... Thank you very much for your helpful response, Steve, especially the comment on DESeq2::vst. You helped me solve the problem I was trying to figure out. ...
written 7 weeks ago by anpham0
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Expression profile from $E from Voom
... Following the voom-limma workflow and using RNA-seq count data, I created the DGEList, ran the calcNormFactor (TMM) step, ran Voom step, and got the v object. I then extracted the $E object from v. Here is my code: x <- DGEList(counts=RNA) x <- calcNormFactors(x, method = "TMM") par(mfrow= ...
voom $elist written 8 weeks ago by anpham0 • updated 8 weeks ago by Steve Lianoglou12k
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RNA-seq differential analysis for continuous phenotypes
... I would like to do a genome-wide differential expression analysis for a continuous phenotype using counts from RNA-seq (raw counts from STAR alignment). Normally I'd use DESeq2 for the analysis and not having to do normalization. However, my understanding is that DESeq2 only models categorical pheno ...
deseq2 rna-seq written 12 weeks ago by anpham0 • updated 12 weeks ago by Michael Love14k
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Comment: A: DESEq2 VST error
... Thank you, you're right. This is a miRNA dataset so there are 767 rows. Would I have another option to do VST with this number of rows?  ...
written 3 months ago by anpham0
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DESEq2 VST error
... I'd like to perform variance stabilization transformation in DESeq2 but got this error message. Any input would be much appreciated. Thank you.   vsd <- vst(dds, blind = TRUE) Error in vst(dds, blind = TRUE) : less than 'nsub' rows,   it is recommended to use varianceStabilizingTransformation d ...
deseq2 variancestabilizingtransformation written 3 months ago by anpham0
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DESeq2 Error: ncol(countData) == nrow(colData) is not TRUE
... I tried to build an DESeqDataSet with a count matrix and a table of sample information. My count matrix is read from a csv file. The count matrix has gene names as the first column. Here are my codes and error message. Please advise as how I should address the error message. Thank you.   # read in ...
deseq2 error written 4 months ago by anpham0 • updated 4 months ago by Michael Love14k
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Comment: C: rlog transformation using DESeq2
... Thank you for the helpful response. I have a follow-up question. Using DESeq2 workflow, I performed rlog transformation on gene-level raw counts to obtain Transformed Gene-level Count (normalized for sequencing depth). Now, can I use the tximport pipeline on this Transform Gene-level Count to obtai ...
written 13 months ago by anpham0
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rlog transformation using DESeq2
... I have some questions about rlog transformation using DESeq2: 1) This transformation normalizes for library size, which is sequencing depth or total number of mapped reads, correct? 2) This transformation does not normalize for gene or transcript length, correct? If this is true, is there a progra ...
deseq2 rlog transformation written 13 months ago by anpham0 • updated 13 months ago by Michael Love14k
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Answer: A: Subset SummarizedExperiment/GRangesList by seqnames
... Thanks very much Michael and Martin.  I used the codes below to subset the dds object and it worked without any problem. seqnames(dds) dds.sub <- dds[ all(! seqnames(dds) %in%  c("chrX", "chrY"))] ...
written 2.6 years ago by anpham0
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Answer: A: remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
... Thank you for your response. I followed the instruction and got an error message and not sure how to fix it. I used the UCSC hg19 to make the count matrix using GenomicAlignments. I copied the codes and the error message here. (By the way, I named my dds "dds1"). Thanks.   csvfile1 <- "table1.c ...
written 2.6 years ago by anpham0

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