User: informatics bot

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Posts by informatics bot

<prev • 75 results • page 1 of 8 • next >
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Comment: C: Bioinformatician for a medical epigenetics project (Freiburg, Germany)
... Would someone with a BA and 3+ years off experience be able to apply? ...
written 2.4 years ago by informatics bot570
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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 2.6 years ago by informatics bot570
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Answer: A: GEO2R not performing log2 transform??
... 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 2.7 years ago by informatics bot570
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Comment: C: I am really pissed off by the bioinformatics software world. Do/can we have a be
... that's a whole different can of worms. ...
written 3.0 years ago by informatics bot570
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Comment: C: I am really pissed off by the bioinformatics software world. Do/can we have a be
... 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 3.0 years ago by informatics bot570
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Answer: A: What is the difference between gene signature , disease signature and drug signa
... 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 3.1 years ago by informatics bot570
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Answer: A: Getting rid of noise in gene expression
... 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 3.1 years ago by informatics bot570
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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 3.1 years ago by informatics bot570
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Comment: C: WGCNA maxBlockSize limit
... I believe OP is using micro-array data not RNAseq ...
written 3.1 years ago by informatics bot570
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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 3.1 years ago by informatics bot570

Latest awards to informatics bot

Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: PCA plot of RPKM data from RNA-Seq dataset
Popular Question 2.8 years ago, created a question with more than 1,000 views. For STAR Aligner minimum read-length
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: I am really pissed off by the bioinformatics software world. Do/can we have a be
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: RNASeq with mixed tissues
Scholar 3.3 years ago, created an answer that has been accepted. For A: PEER normalization after DESeq run
Scholar 3.4 years ago, created an answer that has been accepted. For A: PEER normalization after DESeq run
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: RNASeq with mixed tissues
Supporter 3.5 years ago, voted at least 25 times.
Scholar 3.6 years ago, created an answer that has been accepted. For A: PEER normalization after DESeq run
Scholar 3.7 years ago, created an answer that has been accepted. For A: PEER normalization after DESeq run
Scholar 3.8 years ago, created an answer that has been accepted. For A: PEER normalization after DESeq run
Scholar 3.8 years ago, created an answer that has been accepted. For A: PEER normalization after DESeq run

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