User: gracie

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gracie20
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Posts by gracie

<prev • 17 results • page 1 of 2 • next >
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R data repository to use in shiny app
... I am working on a shiny app which reads lots of fst files (5gb in total) and makes a large list. Is there any r data repository that I can use in shinyapp so when I make it online it can directly get data from there? Thanks in advance ...
R shiny written 5 days ago by gracie20
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differential expression analysis with z score normalized microarray data
... Hi all, I am dealing with a Z normalized expression dataset and I want to perform differential expression analysis with two factor . I tried limma with two factor design (and also single) but couldnt find any gene altered significantly. I am not sure is it because I am violating any assumptions o ...
microarray deg limma written 8 months ago by gracie20 • updated 7 months ago by Biostar ♦♦ 20
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Comment: C: Affymetrix cross platform probe matching
... Clustering based on DEGs basicly and also extracting the genes altered same and opposite direction. I am not planing to do meta analysis because each dataset contains their own control group and I am only intrested in DEGs. ...
written 9 months ago by gracie20
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Affymetrix cross platform probe matching
... Hi all, I have multiple datasets some from hgu133plus2 ( GPL570) and one affymetrix human exon array 1.0st. I wanna compare the DEGs from these two platforms. Is there any cross platform probe matching data for affymetrix or any suggestions to deal with multiple probesets hitting same gene problem? ...
affymetix microarray written 9 months ago by gracie20
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Comment: A: Affymetrix miRNA 4.0 Normalization
... Thank you, I will go with that most probably. ...
written 16 months ago by gracie20
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Comment: C: Affymetrix miRNA 4.0 Normalization
... As much as I know it should be in featureData part but it is empty it only says annotated dataframe. > str(rawData) Formal class 'ExpressionFeatureSet' [package "oligoClasses"] with 9 slots ..@ manufacturer : chr "Affymetrix" ..@ intensityFile : chr NA ..@ assay ...
written 16 months ago by gracie20
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Comment: C: Affymetrix miRNA 4.0 Normalization
... Thank you. The reason I want to extract human only probes is I thought rma results would differ between rma with all probesets vs only human. > rownames(rawData) [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" "16" " ...
written 16 months ago by gracie20
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Comment: C: Affymetrix miRNA 4.0 Normalization
... Thank you for your answer but I could not find a way to filter rawdata with probeIDs. When I extract the row names with probeNames function (probeNames(rawData), it has 346085 probes however array expression data (rawData@assayData$exprs) has 292681 rows. ...
written 16 months ago by gracie20
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Comment: C: Affymetrix miRNA 4.0 Normalization
... Sure, [GeneChip miRNA 4.0][1] it is. There are probes for human mouse and rat. Since using all probes would change RMA and limma results I thought I should use only human probes. [1]: https://www.thermofisher.com/order/catalog/product/902412 ...
written 16 months ago by gracie20
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Affymetrix miRNA 4.0 Normalization
... I am analyzing a GeneChip miRNA 4.0 Array dataset. here is my code; library(oligo) library(pd.mirna.4.0) celFiles <- list.celfiles( full.names=TRUE) rawData <- read.celfiles(celFiles, pkgname="pd.mirna.4.0") eset <- rma(rawData) This gives results for all organism. Is ...
microarray mirna written 16 months ago by gracie20

Latest awards to gracie

Popular Question 7 months ago, created a question with more than 1,000 views. For pathway analysis tools
Popular Question 15 months ago, created a question with more than 1,000 views. For Wig Files to Interval Files
Popular Question 15 months ago, created a question with more than 1,000 views. For pathway analysis tools
Popular Question 22 months ago, created a question with more than 1,000 views. For pathway analysis tools

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