Questions tagged [microarray]
questions involving microarray analysis (e.g. Illumina BeadChip, Affymetrix GeneChip)
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How to annotate Agilent probeIDs and obtain corresponding RefSeqmRNA from NCBI in a microarray analysis in R?
I am working on a microarray analysis using Agilent data (SurePrint G3 Mouse GE 8x60K IDs e.g. A_30_P01020727), having the list of Probe IDs with it´s corresponding statistics and fold changes. My ...
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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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Calculating p-value and adjusted p-value for pre-normalized microarray data with fold change precalculated
I have a microarray dataset with two mutants dataset that has already been normalised, and the fold change values for each gene in each mutant versus the wild type have been calculated. I'm interested ...
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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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Adding BAF and Log2 ratio to VCF file
I have access to pre-processed VCF files from a genetic dataset, and am trying to use the MoChA tool to calculate mosaic chromosomal alterations in this dataset. However, MoChA requires BAF and ...
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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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Allele effects by parental-origin estimated from genotyping array data
We are dealing with relatively large family data (> 1,000 trios) with genotyping array data.
We would like to see the allele effects on children separately of mothers, fathers, and children, as in ...
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Handling of sex chromosomes in male when computing CNV copy ratio
Reading from CNVkit documentation, Mathworks documentation, Bionano documentation, for CNV calling, it seems that the common practice for array is to compute the linear copy ratio by normalizing ...
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