User: Lucia Peixoto

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Lucia Peixoto330
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Posts by Lucia Peixoto

<prev • 32 results • page 2 of 4 • next >
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Comment: C: [Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
... Dear Simon, To obtain my count matrix I use each Ucsc gene model as one " transcript", I limit my comparisons with the microarray data to those Ucsc gene models that have a unique RefSeq match with an Affy probe set Regarding multiple testing, I guess there is no reason why I can't use the uncorre ...
written 6.5 years ago by Lucia Peixoto330
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Comment: C: [Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
... Thanks everyone for the helpful input My counts are in fact total counts per transcript and not averages, my mistake in the original post I have an average of 70 million read pairs of 100bp, with very even number of reads for all my samples I am curious regarding how many clonal reads is too many ...
written 6.5 years ago by Lucia Peixoto330
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[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
... Dear All, I have a dataset for which I have two conditions. I have 9 replicates per group for microarrays, 5 per group for RNAseq (which are a subset of the RNA samples used in the microarrays, couldn't sequence all 9), and 8 per group for qPCR (which is an independent set of experiments). Each n ...
sequencing rnaseq microarray qpcr coverage edger deseq written 6.5 years ago by Lucia Peixoto330 • updated 6.5 years ago by Steve Lianoglou12k
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Comment: C: DESeq2 vs limma/voom: PCA completely different. How to proceed?
... Hi, I have been exploring my data in terms of gene expression in a lot of ways (microarray, RNAseq, qPCR) and for my case it is important to account for the first two PC for analysis of differential expression, which is easy for the microarray data. I am thinking about transforming my RNAseq data, ...
written 6.6 years ago by Lucia Peixoto330
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Comment: C: DESeq estimateDispersions
... HI All, thanks very much for the help, doing local fit fixes the issue I a not sure I understand what is the impact of doing this in terms of the accuracy of the estimates can someone explain? will it affect greatly the number of differential calls at a particular cutoff? thanks Lucia On Wed, Ap ...
written 6.6 years ago by Lucia Peixoto330
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DESeq estimateDispersions
... Hi, I am trying to run DESeq and I keep getting the following error after trying estimateDispersions Error in parametricDispersionFit(means, disps) : Parametric dispersion fit failed. Try a local fit and/or a pooled estimation. (See '?estimateDispersions') I cannot figure out why this is happ ...
coverage deseq written 6.6 years ago by Lucia Peixoto330 • updated 6.6 years ago by Simon Anders3.6k
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EdgeR vs voom, what to consider when deciding which to use
... Dear All, As I continue my exploration of RNASeq analysis options, it seems that some approaches are better than others depending on your data-set and goals. I was wondering if anyone can give me a feeling on when is better to use Voom vs EdgeR (or DESeq) and whether modelling the distribution is re ...
rnaseq qpcr edger written 6.7 years ago by Lucia Peixoto330 • updated 6.7 years ago by Steve Lianoglou12k
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Difference between EdgeR and DeSeq in library normalization
... Dear All, I am currently analyzing an RNASeq dataset, I have 3 samples with n=4 each. I was exploring the performance of both EdgeR and DeSeq and I noticed they vary a lot on the dispersion of the normalization factors. Using EdgeR calcNormFactors I get a distribution that varies from 0.9-1.2 while ...
rnaseq normalization edger deseq written 6.7 years ago by Lucia Peixoto330 • updated 6.7 years ago by Simon Anders3.6k
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Comment: C: edgeR: Value of variation of biological variation (BCV)
... Hi, I had a related question regarding BCV, it has been my recent experience that working in vivo with heterogeneous tissues such as brain yields a much higher BCV than 10%, usually close to 30% even though I am working with genetically identical organisms (mice, all males as well). Is that your obs ...
written 7.3 years ago by Lucia Peixoto330
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edgeR, error in estimateCommonDisp
... Hi All, I am pretty new to edgeR, this is the first time I use the package, as well as the first time I try to find differential expression using RNA-Seq data (this is the first time I have biological replicates). I apologize in advance for my lack of knowledge. I have 10 samples, 5 biological rep ...
edger written 7.3 years ago by Lucia Peixoto330

Latest awards to Lucia Peixoto

Popular Question 5.3 years ago, created a question with more than 1,000 views. For [Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Popular Question 5.3 years ago, created a question with more than 1,000 views. For CDF file for Mouse Gene 1.1 ST Array
Popular Question 5.3 years ago, created a question with more than 1,000 views. For DESeq estimateDispersions
Popular Question 5.3 years ago, created a question with more than 1,000 views. For EdgeR vs voom, what to consider when deciding which to use

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