User: Akula, Nirmala NIH/NIMH [C]

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Posts by Akula, Nirmala NIH/NIMH [C]

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Comment: C: Correcting for known and surrogate variables in DESeq2
... Yes, these are human samples from two different populations. Here's the qq-plot ...
written 8 months ago by Akula, Nirmala NIH/NIMH [C]180
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Answer: A: Correcting for known and surrogate variables in DESeq2
... After correcting for 13 surrogate variables, a QQplot of the observed p-values looks inflated compared to the expected. Here's the code I used: >design(dds.sva)=~SV1+SV2+SV3+SV4+SV5+SV6+SV7+SV8+SV9+SV10+SV11+SV12+SV13+condition > dds.sva <- DESeq(dds.sva)                                   ...
written 13 months ago by Akula, Nirmala NIH/NIMH [C]180
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Correcting for known and surrogate variables in DESeq2
... NHi All, We have RNA-seq data on controls and cases along with known co-variates like race, age, sex, RIN and library batch. So, in DESeq2 I could correct for these covariates as follows: dds=DESeqDataSetFromMatrix(countData=countData,colData=coldata,design=~race+age+sex+RIN+batch+condition) On t ...
deseq2 svaseq written 13 months ago by Akula, Nirmala NIH/NIMH [C]180
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Comment: C: filtering before using DESeq
... Hi, What would be a reasonable/widely used cut-off for overall variance and overall sum? Thanks for pointing out the number format. The example I gave is from eXpress software and I rounded the numbers to closest integer before I input into DESeq. Regards, Nirmala ________________________________ ...
written 4.9 years ago by Akula, Nirmala NIH/NIMH [C]180
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Comment: C: filtering before using DESeq
... Thanks Sean for your response. Regards, Nirmala ---------------------------------------------------------------------- -------------------------------------------------------- Contractor Buiding 35, Room 1A-205 35 Convent Drive, National Institute of Mental Health/NIH Bethesda MD - 20892 Phone# 30 ...
written 4.9 years ago by Akula, Nirmala NIH/NIMH [C]180
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filtering before using DESeq
... Hi, We counted the reads in our RNA-seq data using HT-seq and removed any isoforms that have <5 reads/sample. We then used DESeq for differential expression analysis. Here's an example of a transcript that has the following read counts: GeneA_cases counts: 85.78942 19.11753 1471.813 61.714 ...
deseq written 4.9 years ago by Akula, Nirmala NIH/NIMH [C]180 • updated 4.9 years ago by Wolfgang Huber13k
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Comment: C: HT-seq counting - gene vs isoform
... Thank you very much for your response Simon. Best Regards, Nirmala ---------------------------------------------------------------------- -------------------------------------------------------- Contractor Buiding 35, Room 1A-205 35 Convent Drive, National Institute of Mental Health/NIH Bethesda M ...
written 5.0 years ago by Akula, Nirmala NIH/NIMH [C]180
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HT-seq counting - gene vs isoform
... Hi, I am trying to understand the counting done by HTseq using Ensemble GTF file. Here is an example: GeneA_isoform1: Exon1 Exon2 Exon3 GeneA_isoform2: Exon1 Exon3 GeneA_isoform3:Exon1 Exon4 When counting at gene level, I assume the reads that fall on ...
written 5.0 years ago by Akula, Nirmala NIH/NIMH [C]180 • updated 5.0 years ago by Simon Anders3.4k
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clarification on DEXSeq output
... Hi, Below is the result of one exon that is differentially expressed according to DEXSeq analysis. geneID ENST00000373530+ENST00000290273+ENST00000373529+ENST00000483816 exonID E002 dispersion 2.680e-01 pvalue 0.000 padjust 0.029 meanBase 6.1533324 log2fold(control/case) 3.1516850 Since the ...
dexseq written 5.3 years ago by Akula, Nirmala NIH/NIMH [C]180 • updated 5.3 years ago by Simon Anders3.4k
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error in DEXSeq version 1.3.13
... Hi, I have used DEXSeq (version 1.2.0) successfully to find differentially expressed exons in RNA-seq data. Yesterday I upgraded DEXSeq to version 1.3.13 I get the following error: > ecs=read.HTSeqCounts(countfiles=file.path("/data/DexSeqCounts/",past e(rownames(samples),"txt",sep=".")),design= ...
dexseq written 5.3 years ago by Akula, Nirmala NIH/NIMH [C]180 • updated 5.3 years ago by Alejandro Reyes1.5k

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