Questions tagged [microarray]

questions involving microarray analysis (e.g. Illumina BeadChip, Affymetrix GeneChip)

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Recalculating fold change in microarray from a subset of samples

I have some bulk microarray data that I have pulled from online sources which describes the spatial distribution of transcription. The tissue in question has a few different subregions. I am ...
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20 views

Gene Ontology Specific Fold Changes

I am currently doing a project involving gene rank correlations. How we rank our genes is based on the absolute values of the log2 fold change. I.e. a gene which is doubled with respect to the ...
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1answer
34 views

How to perform DE analysis for each sample

I am new to R and biocondunctor. I have the normalized expression values for 20 samples for a disease and for 10 controls. I wanted to get the differential expressed values for each sample with all 10 ...
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36 views

How could I find Differential Genes in Expression Matrix File by R?

I tried to get gset of my dataset by getGEO function, but unfortunately it didn't work( I installed GEOquery package) and i get errors like this: Found 1 file(s) GSE69606_series_matrix.txt.gz trying ...
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33 views

How can extract the list of genes name from the raw data in GEO?

The format of the raw data that upload in GEO is different, like TXT, CEL or other form. How can I extract the list of genes name from these formats? And then how can I normalize them with R? I would ...
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31 views

A problem in meta-analyzing microarrays

I am working on meta-analysing of microarray data of normal and breast cancer tissues. When I run the combatch, I encounter this error: ...
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1answer
45 views

R error: could not find function “pathwayAnalysis”

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47 views

How can I correctly get 3D scatter plot for micro-array pheno data in R [updated]?

I intend to see data points distribution (each reows) within labeled groups (different batchs such as 1,2,3, and so on) in 3D scatter plot, because I want to see the distribution of the data points ...
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50 views

Any way to filter out highly correlated genes with limma linear model?

I have Affymetrix gene level expression matrix (genes in the rows and sample ID on the columns), and I have annotation data of microarray experiment observation where sample ID in the rows and ...
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1answer
24 views

Any way to quantify the variation of genes that expressed in Affymetrix expression data?

am experimenting preprocessed Affymetrix microarrays expression data matrix (Affymetrix probe-sets in rows (32830 probesets), and RNA samples in columns (735 samples)) for my downstream analysis. Here ...
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41 views

How can I convert Affymetrix microarray data to bedgraph format?

I've previously asked a different question about the ChIP-chip microarray data that I'm working on. I'm new to this so I'm sorry for asking here again. I have .CEL files and I'm using the Affy ...
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1answer
111 views

Extracting expression data in r from GEO and got a S4 object

I want to open the expression data GSE9838 dataset from GEO using GEOquery R package. gset <- getGEO(filename="GSE9838_family.soft.gz") The result of this ...
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131 views

Differentially methylated position analysis in a related sample?

I'm trying to figure out how to do a DMP analysis (using minfi dmpFinder) on a related sample (if it's even possible). Right now the code (not written by me) is: ...
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2answers
42 views

Affymetrix tags (same ID's) present in different places of the genome

could you explain me how to interpret such situation? Same tag aligned in several distint places, near different genes... Is the annotation able to distuinguish such 'same' tags, during DGE analysis? ...
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1answer
112 views

Where can I find .cdf files for Affymetrix ChIP-chip data analysis?

I am analysing microarray ChIP data generated several years ago. I want to use the affy package for R. However, in order to load the CEL files and proceed with the analysis, I need the pombe ...
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1answer
72 views

Combat for multiplatform batch correction

I have been looking ways to use data from various micro-array platform such as agilient, rosetta/merk. Some of the established method I came across is combat, but I'm not sure if it can be done for ...
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1answer
87 views

Question about the dots on Quartile groups in boxplot

I have Microarray Normalized Expression data for a specific Gene. It looks like below in a dataframe B ...
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41 views

Gene not found in Affymetrix expression profiles

I am studying the ABA network in A. thaliana, consisting of HB7, ABI1 and AREB2. The AGI code I was given are, respectively: AT2G46680, AT4G26080 and AT1G45249. I downloaded the following file in ...
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29 views

What are some good sources of 3rd order gene expression data

I need good sources of gene expression data in the form of 3rd order tensors. Typically the commonly available datasets are in the form of a matrix, for instance, $sample \times gene$ or $gene \times ...
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1answer
179 views

Hierarchical models with limma?

I have a dataset with (microarray) gene expression data that was sampled from the same individuals at multiple timepoints. Our exposure is a continuous variable, and because this was an observational ...
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1answer
70 views

How to calculate call detection values in microarray datase if .cel file unavailable

I would like to do a differential gene expression analysis on a microarray data. From the literature, I understood, call detection (Present, Absent, Marginal) has to be done to minimize false ...
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1answer
188 views

What is a standard approach to binarize microarray gene expression data?

I am using gene expression data from a microarray dataset for the purpose of learning the network structure of genes in the dataset. Now to do this I need to binarize my data, i.e convert the data ...
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1answer
48 views

coexnet package for network co-expression analysis, is looking for a filelist.txt that doesn't exist

On my way to create a co-expression matrix for a microarray experiment, using the coexnet package I had to use a function called ...
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1answer
79 views

Classification (supervised learning) of expression data on pathway level

I was wondering if there is any way to apply classification algorithms (e.g random forest) on microarray data but not using the genes as predictors/features but the pathway they belong to. The thing ...
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1answer
77 views

How hard is it to clean and QC gene expression microarray data?

I am a PhD student working on developing ideas for my dissertation papers. One of my planned papers will be working with some (human) gene expression data. I have had a class on working with gene ...
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45 views

Pathifier bioconductor package recommends to use technical noise for an argument. How to determine it?

I'm running the pathifier approach against C2 pathway curated database for a specific microarray dataset. As I was reading the documentation of the pathifier, in order to configure it properly for ...
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1answer
58 views

Integration of different microarray dataset to run GSEA

I'm planning to run a GSE Analysis on some microarray datasets. Until now what I have done is to pre-processed them using frma algorithm. The reason I chose frma instead of gcrma or rma is that I ...
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1answer
173 views

Interpreting large z scores from microarray data

I have microarray z scores for gene set enriched (GSE) pathways that range approximately from -3 to 14. I understand that an absolute value of 1.96 has a p-value = .05 and significant for our purposes....
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2answers
449 views

Normalizing microarray data for clustering heat map

I wanted to generate a clustering heat map for the microarray data. This is the first time I'm working on Microarray data. I read some tutorials but have few doubts. I'm using microarray (Affymetrix ...
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1answer
32 views

Simple Affy Differential Expression

I think I have a fairly easy-to-solve problem. I have an expression table generated from an Affy set. It has one row of gene names (already symbols) and then 180 sample rows. 181 rows total. So I ...
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1answer
124 views

error in heatmap using R

I am learning about generating heatmaps using R. For this example I am using randomly generated data to test the process, but I encountered what appears to be an error or perhaps there is something am ...
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1answer
75 views

Standard Cutoff for Moderated T-statistics

I'm looking at some microarray data. For the first time I've calculated a moderated T statistic from limma. Is there any standard practice for where to cut off that value? For log2 fold change I ...
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1answer
48 views

Differences between NetAffx Hg-U133 Plus 2.0 Annotation file versions

From what I was able to observe, the annotation files (CSV) for NetAffx Hg-U133 Plus 2.0 is updated regularly. However, from glancing at the CSV files (NA35: 2015 & NA22: 2007), I can't seem to ...
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628 views

Using the t-SNE algorithm on microarray data + an error bonus

I'm trying to use the t-SNE algorithm on some microarrays data. More specifically my data frame has 18600 columns with genes (features) and 72 rows with conditions with replicates ( 10xWt , 10xTg , ...
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1answer
3k views

Extracting expression data from GSE dataset downloaded from GEO

I have downloaded GSE16146 dataset from GEO using GEOquery R package. I would like to extract "Data table" from downloaded GSE16146. ...
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1answer
77 views

How can I combine a kinship matrix with subset individuals when using rvtests?

I've been processing data for a consortium project that uses the rvtests toolkit. Our data analysis process uses a kinship matrix and the calculation of inverse-normalised transformed statistics after ...
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1answer
336 views

What are some good practices to follow during EPIC DNA methylation data analysis?

I recently got some EPIC DNA methylation data and I was wondering what are some good practices to follow? I am interested in knowing about normalization and differential analysis. Thank you.
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3answers
364 views

probeset to probeset mappings between Affymetrix arrays

I am interested in identifying mappings between different types of Affymetrix arrays. I am aware that mappings between gene and probeset can be extracted using Ensembl's Biomart database. ...