User: pepere

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pepere40
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Posts by pepere

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Comment: C: Uncertain about PCA plot for DESeq2 analysis
... Thanks for the quick reply. My main concern was not seeing differences with the healthy controls. We did a similar experiment in the past with another drug and differences in the PCA and DE were evindent. I performed the DE analysis using this coldata: Sample Patient Responder Time Control m01 1 ...
written 8 months ago by pepere40
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Uncertain about PCA plot for DESeq2 analysis
... Hi, I have a RNA seq dataset obtained from patients treated with a specific drug (The sequencing data is of very good quality), they are separated into 3 groups: healthy controls, good responder patients and bad responder patients (patients samples are also further divided into pre-treatment and pos ...
rnaseq deseq2 bioconductor pca written 8 months ago by pepere40 • updated 8 months ago by Michael Love25k
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Comment: C: DEXseq ignoreRank
... works fine now, thanks On 12 May 2014 16:03, Michael Love wrote: > Fair enough. > > Could you try reinstalling DESeq2? The error is R reporting that this > function doesn't have an argument which it should have in v1.4. > > Mike > > > On Mon, May 12, 2014 at 9:51 AM, M ...
written 5.4 years ago by pepere40
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Comment: C: DEXseq ignoreRank
... mmm....have a look :P > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 ...
written 5.4 years ago by pepere40
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DEXseq ignoreRank
... Hello, i get this strange error: dxd = DEXSeqDataSetFromHTSeq(countFiles,sampleData=sampleTable,design= ~ sample + exon + condition:exon,flattenedfile=flattenedFile ) Error in DESeqDataSet(se, design, ignoreRank = TRUE) : unused argument (ignoreRank = TRUE) it seems to be an internal error of ...
written 5.4 years ago by pepere40 • updated 5.4 years ago by Michael Love25k
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DEXSeq update results change
... Hello, After performing a general Bioconductor update to the new version, I noticed that now the DEXseq package 1.8.0 is giving me different results from prrevious version 1.6.0. As a start, its function print dots "..." on the stdout which was not done in the previous version. This is not a big iss ...
dexseq written 5.5 years ago by pepere40 • updated 5.5 years ago by Alejandro Reyes1.7k

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