User: Natasha

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Natasha30
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Posts by Natasha

<prev • 84 results • page 1 of 9 • next >
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Comment: C: Plotting gene expression values from microarray data
... I replaced the last line with `ggplot(data = edata,aes(x=colnames(edata)[1]))+geom_density(alpha=.2)` .I couldn't succeed in obtaining a distribution though.![https://image.ibb.co/bVijN9/im.png][1] Is it appropriate to use `geom_density`? [1]: https://image.ibb.co/bVijN9/im.png ...
written 8 months ago by Natasha30
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Plotting gene expression values from microarray data
... I'm trying to plot a distribution graph of the gene expression values,after and before normalization, from microarray data. Here is my code to obtain a plot of the normalized values, library(Biobase) library(GEOquery) library(magrittr) library(rJava) library("xlsx") library ...
gene expression R bioconductor ggplot2 microarray written 8 months ago by Natasha30 • updated 8 months ago by Devon Ryan90k
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Comment: C: Multiple probe for same gene
... Thanks a lot for clarifying all the naive doubts that I ask. I'm facing challenge in interpreting the row indexes of `metadata`. The numbers in the index running from 1 to 10 , do these represent the sample id's? Is it something like? metadata condition experiment GSM ...
written 8 months ago by Natasha30
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Comment: C: Multiple probe for same gene
... This clarifies many of my confusions. Thank you very much. Based on the suggestions that was given [here][1], I'm trying to normalize the data from 2 experiments. downloadedAffyFiles <- list.files(path = "../GSE_RAW/", pattern = "CEL.gz$",full.names=TRUE)#53454 AffyData <- ReadAffy(f ...
written 8 months ago by Natasha30 • updated 8 months ago by Kevin Blighe42k
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Comment: C: Multiple probe for same gene
... Thanks a lot for the explanation. Could you please let me know whether it's possible to get the phenoData from the expression set created using CEL files? I tried pData(eset), but it didn't help. Should it be created manually, like the example shown [here][1]? [1]: https://www.bioconductor.org/h ...
written 8 months ago by Natasha30
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Comment: C: Using Limma to normalize data sets from microarray studies
... Hi, I had a chance to look at section 6.2 before. The section heading mentions it's for two color data. The data set that I have is one color data. Also, I couldn't understand how the target file that is used to create `RG` in the syntax mentioned by you has to be generated. In my case, rownames(exp ...
written 8 months ago by Natasha30
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Comment: C: Using Limma to normalize data sets from microarray studies
... Hope I made all the changes ...
written 8 months ago by Natasha30
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Using Limma to normalize data sets from microarray studies
... I'm using Limma to normalize Affy data sets from 2 experimental studies performed using microarray , To check whether the steps that I follow is correct, I am checking whether the box plot that I obtain after processing the RAW file is the same as the boxplot obtained from GSE. GSE: library(Bi ...
gene microarray written 8 months ago by Natasha30
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Comment: C: Multiple probe for same gene
... Kevin, Probably, I'm in the same position now, a beginner asking a lot of silly questions. But thanks to everyone on this forum for being so supportive. I wouldn't have reached this far otherwise. I wish to ask for a few clarifications on the syntax given in the above [link][1] in the context of th ...
written 8 months ago by Natasha30
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Comment: C: Multiple probe for same gene
... Kevin, Thanks a lot for the advise. I had a chance to read through some of the other answers on this same question.Some of the answers were posted six years back. I'm curious to know if there a programmatic way of doing these checks .In an answer given [here][1] ,Robert Gentleman has mentioned abou ...
written 8 months ago by Natasha30

Latest awards to Natasha

Popular Question 8 months ago, created a question with more than 1,000 views. For Identify Transcription factor from a list of genes
Popular Question 8 months ago, created a question with more than 1,000 views. For Interpreting distance from clustal omega

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