Questions tagged [microarray]
questions involving microarray analysis (e.g. Illumina BeadChip, Affymetrix GeneChip)
73 questions
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Normalisation of GEO miRNA microarray data
I am working on a project with 2 datasets, GSE139031 and GSE112264, which are microRNA microarray datasets. I downloaded and ran the data processing from SOFT files to obtain expression data. In this ...
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affy::rma results doesn't match with ncbi website
I'm trying to find out how RMA normalized signal intensity values in this sample have been calculated. I tried to perform RMA in R, but the results are different
<...
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Merge RNAseq and Microarray count datasets
I have two expression datasets:
one RNA-seq dataset downloaded from Expression Atlas (raw counts)
another Microarray dataset containing normalised intensities
These two datasets contain the same ...
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WGCNA sample-data preprocessing order
I was trying to do WGCNA analysis for microarray data. The raw data was processed by "MAS5.0 Scaled 100 generated expression value". In the prepocessing step, I am seeing is 3 levels of ...
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Meta-analysis with 2 GEO transcriptomic datasets possible?
I was searching for a set of keyterms in the GEO database. After making my PRISMA chart I ended up having 2 datasets only. My Question is can proceed with aggregating those 2 microarray datasets and ...
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Inconsistent microarray expression levels after normalizing with log2
I know it is necessary to normalize the GEO microassay data before analysing. Howerver, after using log2 to normalize the data and checking with boxplot, I found the data is still not align in the ...
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When analysing microarray data, is it need to do normalization and standardization both?
When we do differential expression analysis, it is common to normalize the data using a log transform:
exprs(gse) <- log2(exprs(gse))
This ensures that the ...
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Practical challenges for microarray analysis and single cell
currently, I am learning single-cell sequencing and microarray analysis. I am searching for somewhere (or any alternative way)to practice and get hands-on with these techniques. please help me with ...
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GSEA vs GSVA: Pros and cons of each method
Trying to understand when GSEA is more appropriate than GSVA and vice versa. I have seen cases when running GSEA and GSVA on the same task - compare enrichment of a geneset between two groups - gives ...
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Does using a microarray chip that matches the chip used in training lead to higher explained variance of a polygenic score?
I'm trying to replicate an existing polygenic score (i.e. test the accuracy in a new sample), and want to know if matching the original study's microarray chip will improve the accuracy (that is, ...
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Does pooled sample genotyping microarray analysis exist?
I want to genotype samples in small batches with a common microarray (e.g., the GSA). However, the cost is very high for small batches.
With a higher sample throughput/volume, per sample cost becomes ...
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Does phasing improve imputation quality?
If so, by about how much? I want to know the downsides of skipping the phasing step on human microarray and WGS data.
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illuminaHumanv2.db returning NA for all Illumina probe ID to gene symbol conversion [closed]
This question has been cross-posted on Biostars but has not received any answers yet, so I'm posting it here. I'll update here if it gets answered there.
I have downloaded a miRNA expression dataset ...
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DESeq2 throwing error while normalizing raw microarray expression data due to presence of negative values
This question was also asked on Biostars
I am trying to download and analyze a miRNA expression dataset from NCBI GEO (GSE25631). I specifically want non-normalized ...
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Should I compensate for two clusters of samples in microarray by hierarchical clustering and MDS?
I seem to have two groups of samples based on hierarchical clustering as well as MDS plot analysis using the sample label from the tree cut of the hierarchial clustering. I am analyzing microarray ...
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