User: Davis, Wade

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Davis, Wade350
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Posts by Davis, Wade

<prev • 33 results • page 1 of 4 • next >
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Answer: A: How does MEDIPS handle multiple mapping of a read
... Hi Allen, It seems there are two somewhat related issues that are relevant here: multi-mapped reads (i.e., NOT uniquely MAPPABLE read) and duplicate reads (i.e., not the only read with a given same start/stop). I like to avoid the term "unique" by itself because it can be ambiguous as you can see. ...
written 5.1 years ago by Davis, Wade350
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Answer: A: External RNA controls on Rat Gene ST 2.0 chip lfc ~ 1 after xps rma??
... Matt, Here are some comments that may be helpful, but they don't directly address your question... The "Subgroup B" ERCC spike-ins *should* have lfc=0. I like to look at that group first. I also like to look at the raw data "within subject" across the (log) concentration range and see where the li ...
written 5.2 years ago by Davis, Wade350
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Comment: C: EdgeR: replicated pools, yes or not?
... I'm glad you are aware of the Kendziorski et al. paper, because it is the most applicable to the concept of biological vs. mathematical averaging. Also, I agree with Ryan. Several years ago I did exactly what he mentioned, looking in silico pooling vs. actual pooling, along with extensive simulatio ...
written 5.4 years ago by Davis, Wade350
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Comment: C: Voom Normalization and negative numbers
... It’s not a perfect analogy, but the end is the same: you have a negative number that represents an expression level, and that is my point. In the qPCR example, it would be because the difference between the reference and the target; in log cpm, it is because the expression is low. The reason for ...
written 5.5 years ago by Davis, Wade350
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Comment: C: Voom Normalization and negative numbers
... There should be no conceptual problems with comprehending negative expression values, aside from the strange look collaborators may give you the first time they encounter it. But this is really not much different from Q-PCR experiments when the ∆Ct level for the target gene is more abundant than t ...
written 5.5 years ago by Davis, Wade350
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Answer: A: Voom Normalization and negative numbers
... Hi Micheal, As described in the help file (?voom) the $E component of the output object contains a "numeric matrix of normalized expression values on the log2 scale". So negative values indicate low levels of (normalized) expression. Even though your filtering step filters out genes with 14 or les ...
written 5.5 years ago by Davis, Wade350
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Answer: A: Normalization of RNAseq data using ERCC?
... Hi Agnes, I have used ERCC spike-ins in a large RNA-Seq study (600+ samples). I would temper expectations for any approach based on them. The dynamic range of the spike-in is large (I recall 18 orders of magnitude on base 2 scale), so unless you are sequencing quite deeply, don't get high read count ...
written 5.6 years ago by Davis, Wade350
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Comment: C: BiomaRt Ensembl RefSeq query error
... Georg, Using your code and calling for only "ENSMUSG00000000567" does not result in NA for me, as you can see: library(biomaRt) ensembl <- useMart("ensembl", dataset = 'mmusculus_gene_ensembl') getBM(attributes = c("ensembl_gene_id","refseq_mrna"), filter="ensembl_gene_id", ...
written 5.7 years ago by Davis, Wade350
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Comment: C: scholarly reference for "don't draw PCA/heatmap dendrograms on DEGs"
... I second the comment made by Aaron. I use PCA only for QC discovery and exploration prior to any testing for DEGs. I also agree with the original comment about it being a self- fulfilling prophecy (not that it always turns out that clearly). Anyone thinking that PCA plots based on DE features (obtai ...
written 5.8 years ago by Davis, Wade350
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Advice to RIPSeeker users to improve RAM and CPU use
... I strongly recommend those using the RIPSeeker library to take advantage of the parameters minBinSize and maxBinSize when using the RIPSeek function. For one pair of bam files (RIP and control), I didn't set any limits on minBinSize and maxBinSize, and it used more than 300GB of RAM. CPU time : 14 ...
ripseeker written 6.0 years ago by Davis, Wade350

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