User: informatics bot
informatics bot • 610
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Posts by informatics bot
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... Would someone with a BA and 3+ years off experience be able to apply? ...
written 3.0 years ago by
informatics bot • 610
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Answer:
A: PCA from kallisto output
... My lab takes the estimated counts, rounds them to the nearest integer, performs VST normalization using the DESeq2 package, then plots the first two PC coordinates from the prcomp() function.
...
written 3.2 years ago by
informatics bot • 610
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90
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... LogC is a boolean variable used to check if the quantiles had previously been normalized or transformed.
the if statement:
if (LogC) { ex[which(ex <= 0)] <- NaN
exprs(gset) <- log2(ex) }
checks to see if the data is already normalized/transformed. If the data isn't pre-normailz ...
written 3.3 years ago by
informatics bot • 610
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... that's a whole different can of worms. ...
written 3.6 years ago by
informatics bot • 610
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... I agree.
Bioinformaticians **must** have an in depth knowledge of the biology and biotechnology they are working with. Otherwise they are vulnerable to making mistakes and using the wrong tools. This knowledge can only be obtained after years of debugging, troubleshooting, and decision making. ...
written 3.6 years ago by
informatics bot • 610
1
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... Disease signature is usually a list of genes, within a specific tissue, that are up or down regulated when compared to healthy controls.
Gene signature is a group of genes in a cell whose combined expression pattern is uniquely characteristic of a biological/cellular/molecular phenotype (i.e. cilia ...
written 3.7 years ago by
informatics bot • 610
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... There are many ways to reduce noise in RNA-seq gene expression data. I personally have found the following approach useful when dealing with heterogeneous tissue and >100 samples.
1.) Remove genes with low gene expression.
2.) Remove samples that lack adequate sequencing depth (My lab usually s ...
written 3.7 years ago by
informatics bot • 610
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Answer:
A: IPA Core analysis
... You don't "need" the log fold change values, however, they add statistical power to your IPA analysis (i.e. make your results more accurate). You do not need to convert the log fold changes generated with EdgeR. I would run core analysis with only large intestine, and then try it with other cell typ ...
written 3.7 years ago by
informatics bot • 610
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Comment:
C: WGCNA maxBlockSize limit
... I believe OP is using micro-array data not RNAseq ...
written 3.7 years ago by
informatics bot • 610
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2.2k
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Comment:
C: WGCNA maxBlockSize limit
... You didn't answer my question. How much memory is on the node you're using? ...
written 3.7 years ago by
informatics bot • 610
Latest awards to informatics bot
Good Answer
2.9 years ago,
created an answer that was upvoted at least 5 times.
For A: PCA plot of RPKM data from RNA-Seq dataset
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For C: I am really pissed off by the bioinformatics software world. Do/can we have a be
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3.4 years ago,
created a question with more than 1,000 views.
For STAR Aligner minimum read-length
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For C: I am really pissed off by the bioinformatics software world. Do/can we have a be
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For C: I am really pissed off by the bioinformatics software world. Do/can we have a be
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4.0 years ago,
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For A: PEER normalization after DESeq run
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For A: PEER normalization after DESeq run
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For A: PEER normalization after DESeq run
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For A: PEER normalization after DESeq run
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For A: PEER normalization after DESeq run
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For A: PEER normalization after DESeq run
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