User: polemiraza

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polemiraza60
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Posts by polemiraza

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Answer: A: ComBat to remove batch effects from RNA Seq data
... Dear kerrypop, It depends on your task. If you want calculate differential expression it is better use directly raw counts [you should include batch variable in calculations] - please see Edger package / "Users guide" /section 3.4.3 and 4.2 If you want to perform (for example) unsupervised cluster ...
written 3.1 years ago by polemiraza60
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Comment: C: Get Gen-Expression values accross samples for ONE Gene given by Gene-Symbol
... bi_Scholar, If there is kind of restriction for small sample groups in collapseRows function I propose you even better solution. You need to normalize your data (from the raw .cel files) using custom annotation package [ I recommend Brainarray package].  Here is explanation why: http://bmcbioinfo ...
written 3.2 years ago by polemiraza60
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Comment: C: Get Gen-Expression values accross samples for ONE Gene given by Gene-Symbol
... Hey bi_Scholar, AD.2 Usually two or more probesets are homologus to a different regions of the same gene transript. Nevertheless, to help you more efficiently I would like to know what is your array platform, how many samples and sample groups (phenotypes) do you have? Cheers, Pawel ...
written 3.2 years ago by polemiraza60
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Answer: A: Get Gen-Expression values accross samples for ONE Gene given by Gene-Symbol
... Hello bi_Scholar, I think that collapsing (aggregating)  several probe measurements corresponding to a single gene would be the best solution. I recommend collapseRows function in WGCNA package (you can use matrix or data frame as an input). There are a number of useful  options by which you can a ...
written 3.2 years ago by polemiraza60
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Comment: C: What type of data normalization for multiple microarrays?
... Try https://www.bioconductor.org/packages/release/bioc/html/inSilicoMerging.html Best, Pawel ...
written 3.2 years ago by polemiraza60
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geNetClassifier Error in (function (cl, name, valueClass)
... Dear All, I noticed the error in geNetClassifier when using my own dataset which halts the execution. The same error appears when executing data and the code from the vignette [I ommited only translation of Ensembl gene IDs into Gene Symbols which is optional]. I will appreciate your help in resol ...
software error genetclassifier written 3.2 years ago by polemiraza60
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HTqPCR limma decide test issue?
... Dear All, I noticed some confusing meanTarget/meanCalibrator relation to Limma decide test (-1/0/1) in HTqPCR package. 1. I executed "example preprocessed data" from "qPCR analysis in R" vignette - code below. I extracted whole DE table and "summary" table. I've created the table that refers only ...
htqpcr limma decide test written 3.2 years ago by polemiraza60
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Answer: A: What type of data normalization for multiple microarrays?
... Hello, People assume of "what is batch" depending on their capabilities and/or precaution (it can be chip scan date*; dataset, microarray platform). Batch adjustments may significantly bias  group (phenotype) differences if your study design is unbalanced (groups are not evenly distributed across b ...
written 3.3 years ago by polemiraza60
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Answer: A: What type of data normalization for multiple microarrays?
... Cześć Ewelina, Please clarify: Substracted means extracted? 14 datasets means 14 independent experiments (consisted of some number of samples, each)? What kind of platforms they represent? Best, Pawel ...
written 3.3 years ago by polemiraza60

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