User: Lucia Peixoto

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Lucia Peixoto330
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Posts by Lucia Peixoto

<prev • 32 results • page 1 of 4 • next >
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Answer: A: Steps of removing batch effects and hidden variables
... Hi Shirley, I always have problems with hidden variables, it's the nature of the biology I work with. However, in my experience, there's no such thing as a routine way to remove batch effects. I caution against a "one size fits all" pipeline, every biological question tends to be unique because the ...
written 5.3 years ago by Lucia Peixoto330
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Comment: C: No significant p-values
... Hi Dave, I assume you have only plotted PC1 vs PC2, you can do the same type of plots PC1 vs PC3, PC1 vs PC4 and so on...., to see if any PC captures the grouping by treatment This is regardless of how much variance each PC explains. I usually don't use not DESeq to do the PCA plots, so I am not s ...
written 5.4 years ago by Lucia Peixoto330
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Answer: A: No significant p-values
... Hi Dave, If in your PCA your samples do not cluster by treatment, you likely have some sort of unwanted variation or batch effect masking the effect of the treatment in your data. I am not sure more samples will help. Have you taken a look at the PC loadings past 1 and 2 to see if there is any PC t ...
written 5.4 years ago by Lucia Peixoto330
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About ChIPpeakAnno
... Thanks Julie, this does the job a "shortestDistance" option will be very helpful in the future at least in my data (mouse) it happens a lot for very long genes with multiple splice forms that peaks get assigned to the wrong gene based just on the "canonical" TSS Lucia On Sat, Mar 22, 2014 at 1 ...
mirna chippeakanno written 5.6 years ago by Lucia Peixoto330 • updated 5.6 years ago by Julie Zhu4.1k
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About ChIPpeakAnno
... Hi Julie, I have run ChIPpeakAnno without any size constraints to see what happened. It seemed to be running fine, but when I went to look at my positive controls I realized that it is not annotating all the intragenic peaks as "inside" For example, I have a peak in chr15 89378450 89379100 (mm9) a ...
mirna chippeakanno written 5.7 years ago by Lucia Peixoto330 • updated 5.7 years ago by Julie Zhu4.1k
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About ChIPpeakAnno
... Hi, This is my first time using the package, so maybe this is a naive question What is the distance cutoff used to find "nearest feature (gene, exon, miRNA,etc)" or there isn't any and I can filter on it after the mapping? thanks -- Lucia Peixoto PhD Postdoctoral Research Fellow Laboratory of Dr. T ...
written 5.8 years ago by Lucia Peixoto330 • updated 5.8 years ago by Julie Zhu4.1k
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Answer: A: DEseq for chip-seq data normalisation
... Hi Giuseppe, Unfortunately there is not much available to do stats on ChIPseq data. It is my experience that the data shows exactly the same overdispersion problem that is see in RNAseq so using either EdgeR, DEseq or DEseq2 to analyze ChIPseq data is the way to go. There are a couple of challenges ...
written 6.1 years ago by Lucia Peixoto330
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Comment: C: do we need remove PCR duplicate before we look for DE genes
... Hi Simon, I wonder what your take is on ChIPseq experiments and duplicate removal I tend to cover about 10% of the genome with both RNAseq and different types of ChIPseq, but I am not sure what the dynamic range is for the second and what the effect will be Thanks Lucia Sent from my iPhone On Jun ...
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?
... Hi Wolfgang, Thanks for the apologies. In terms of the data quality, I am pretty confident in the sample collection.As a background, this pair of samples (FC v CC) was extracted from a much bigger timecourse done by microarrays. These are mice, the tissue is brain and I am measuring response to ...
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?
... Dear Simon, My apologies for not being concise in explaining the problem. I am pretty new to the list and I can see that it can be frustrating to try to help someone that is not giving all the details you need to do so. I appreciate your apology, since some of the initial responses to my question h ...
written 6.5 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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