User: bi_Scholar

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bi_Scholar0
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Posts by bi_Scholar

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Log-Transform Values of eSet
... Hello svlachavas, I'm using the Illumina GPL8432 platform. The Data is quantile-normalized but not log2-transformed. As mentioned above, I manually log2-transformed the normalized values in order to use limma. Is this a bad thing?   Thanks for taking your time, M ...
written 12 months ago by bi_Scholar0
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Answer: A: Log-Transform Values of eSet
... Well, I think I have found the solution, sorry for bothering you guys. exprs(eSet) <- log2(exprs(eSet))     ...
written 13 months ago by bi_Scholar0
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Log-Transform Values of eSet
... Hello, I downloaded a GSE file from GEO and converted it to an expression-set using GEOquery. However, even though the values are normalized, they are not log-transformed which is kind of bad, since I'm using limma to analyse the samples. Is it possible to log-transform the values of an eSet direc ...
limma geoquery bioconductor expressionset written 13 months ago by bi_Scholar0 • updated 13 months ago by svlachavas570
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Comment: C: limma; Only fit list of certain genes/ filter eSet
... Perfect. Thanks alot! ...
written 13 months ago by bi_Scholar0
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limma; Only fit list of certain genes/ filter eSet
... Hello, I got a list of genes (<1000) for which I want to perform DEG-Analysis. Since I'm only interested in certain genes, I want to filter out the rest to reduce false-negative results and get more information about the genes I'm actually interested in. Is there a simple way to do this with li ...
limma differential gene expression filter genelist written 13 months ago by bi_Scholar0 • updated 13 months ago by Gordon Smyth32k
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Comment: C: Get Gen-Expression values accross samples for ONE Gene given by Gene-Symbol
... Hey Pawel, thanks for taking time to answer my questions, I really appreciate it! I'm working with an Affymetrix Dataset, downloaded from GEO on the GPL96 platform (HG-U133A). The Samples are grouped by disease-state (healthy/infected) with 5 samples each. I want to analyze the Data for Gene-Coexp ...
written 13 months ago by bi_Scholar0
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Comment: C: Get Gen-Expression values accross samples for ONE Gene given by Gene-Symbol
... Hey Pawel, thanks alot for the answer. I looked into this function and it seems like it is exactly what I was looking for. However, I have two questions regarding the function: 1. The method states, that collapsing methods "maxMean", "Average", etc. are unreliable for 5 or fewer samples, why is th ...
written 13 months ago by bi_Scholar0
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Get Gen-Expression values accross samples for ONE Gene given by Gene-Symbol
... Hello, is there an easy way to query an annotated Expression-Set by Gene-Symbols etc. to extract the Expression-Values for a single gene? I tried to annotate the row-names of the Expression-Matrix with a list of Gen-Symbols obtained from the annotation-file, but as some Gen-Symbols are duplicates, ...
bioconductor expressionset written 13 months ago by bi_Scholar0 • updated 13 months ago by polemiraza40
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Comment: C: limma decideTests results; how to get/sort most significant Genes?
... Hey Alex, I've checked out topTable() and it is indeed what I was looking for. However, what if I choose 'global' as a method for decideTests() ? From my understanding, the Significant Genes found by topTable() and decideTests() could vary in this case. As topTable() ranks Genes by F-Statistics, cou ...
written 13 months ago by bi_Scholar0
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Comment: C: Installing problem Bioconductor
... Alternatively you could try to run R/RStudio in as Admin. ...
written 13 months ago by bi_Scholar0

Latest awards to bi_Scholar

Scholar 13 months ago, created an answer that has been accepted. For A: Log-Transform Values of eSet

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