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

Converting your data.frame to a matrix (and then removing the data.frame) will often free up ...
Devon Ryan's user avatar
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9 votes
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probeset to probeset mappings between Affymetrix arrays

If your question is: can probeset IDs from different platforms be mapped to one another in a similar way as mapping probesets to genes, then the answer is: Yes. BioMart allows you to map almost ...
neilfws's user avatar
  • 656
8 votes

Extracting expression data from GSE dataset downloaded from GEO

According to the manual, all you need to do is: library('GEOquery') gseGSE16146 <- getGEO('GSE16146', GSEMatrix=FALSE) As explanation, ...
aechchiki's user avatar
  • 2,676
8 votes

error in heatmap using R

You have scale="col" in the code. What you are plotting is the z-score calculated based on the value distribution per column. Try changing it to ...
Kraken's user avatar
  • 405
7 votes

probeset to probeset mappings between Affymetrix arrays

Instead of biomaRt, it is also possible to use the mapping databases built into Bioconductor itself, and map from probe to gene, and then from gene to probe in the second. Some R code to convert ...
rmflight's user avatar
  • 191
6 votes
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What are some good practices to follow during EPIC DNA methylation data analysis?

EPIC data can be processed in the same manner as the previous iteration of methylation array data from Illumina (450k). This means that starting with .idat files, normalization should be performed (...
Ben D.'s user avatar
  • 397
6 votes
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Classification (supervised learning) of expression data on pathway level

Have a look at the GSVA package. It allows to convert a matrix with genes x Samples to a pathways x Samples using several ...
llrs's user avatar
  • 4,713
5 votes
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Normalizing microarray data for clustering heat map

You see negative values with your function because you're setting the average of each row to 0 and its standard deviation to 1. In general, I would trust a standard normalization method (rma in this ...
Devon Ryan's user avatar
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5 votes
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Does phasing improve imputation quality?

Yes. Phasing data leads to a better imputation accuracy. More specifically: Improves allele matching: Correct phased data ensures that alleles are matched correctly between the reference panel and ...
JRodrigoF's user avatar
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3 votes
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Combat for multiplatform batch correction

Usually with microarrays you want to make a case/control comparison, so I am going to assume that. Data from different array platforms is generally difficult to compare: each platform is measuring ...
Jay Moore's user avatar
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3 votes
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Question about the dots on Quartile groups in boxplot

You add the points with geom_point(). Just remove it and you will get your "empty" boxplot. ...
Mr_Z's user avatar
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3 votes
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Hierarchical models with limma?

Yes, you can use limma for this mixed model approach. Like you suggest, the random effect (persons) can be put in duplicateCorrelation(). Here is a similar example with RNAseq data, on bioconductor ...
benn's user avatar
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3 votes
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Standard Cutoff for Moderated T-statistics

You're misinterpreting the moderated T-statistic, it's basically the fold-change divided by its variance. The p-value comes directly from that, so if you filter by moderated fold-change you're just ...
Devon Ryan's user avatar
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3 votes
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Calculating mean accross rows with repeated entries in R

Using group_by from dplyr You can use group_by function from ...
dc37's user avatar
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3 votes
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How to check if a given gene is expressed in a group of microarray samples if I do not have control group to compare with?

You ask about which "genes are expressed" and then you mention "if a gene is up or down regulated". These are different, and given your application I think what you actually want ...
user1799035's user avatar
2 votes
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Differences between NetAffx Hg-U133 Plus 2.0 Annotation file versions

After checking the files myself, it does seem like gene identifiers indeed have been updated. Some that were missing have been added with identifiers and some have additional identifiers now. Among ...
AlwaysTrying44's user avatar
2 votes
Accepted

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

Adam Locke (a collaborator of this project) suggests that removing covariate information for the unselected individuals (i.e. setting it to NA) works around this problem: I believe the problem is ...
gringer's user avatar
  • 14.3k
2 votes

probeset to probeset mappings between Affymetrix arrays

Other answers explain why there might not be one to one mapping between the probes. The AbsID database does conversion based on mapping the probe sequences to a genome build, and then determines ...
rmflight's user avatar
  • 191
2 votes

Integration of different microarray dataset to run GSEA

It makes more sense to evaluate by separate the pathway or gene set you want and see if in the three datasets result in a coherent message than to merge these datasets, as you will mix batch effects ...
llrs's user avatar
  • 4,713
2 votes

Interpreting large z scores from microarray data

This is a statistical question. What a higher z value means is that it is more extreme (if you assume a normal distribution), thus a more extreme value is less likely to happen by chance. Which is ...
llrs's user avatar
  • 4,713
2 votes
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How hard is it to clean and QC gene expression microarray data?

I am not sure how much you know about bioinformatics already, can you use R? For a bioinformatician looking at QC for microarrays should not be a big deal, at least for me it would take maybe a day (...
benn's user avatar
  • 3,571
2 votes

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

Based on the info you provide, ArrayBin R package provides you the necessary tools: binarize.array() from ArrayBin, allowing: Implementation of an adaptive ...
aechchiki's user avatar
  • 2,676
2 votes
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Affymetrix tags (same ID's) present in different places of the genome

Is the annotation able to distinguish such 'same' tags, during DGE analysis? No, you'll end up discarding such probes (assuming you have a reason to actually use microarrays still). Why aren't ...
Devon Ryan's user avatar
  • 19.6k
2 votes
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Any way to filter out highly correlated genes with limma linear model?

The problem is that you are transposing the vector of GA values with t(ano$GA). Why would you do that? It produces a row matrix that is inappropriate for input to <...
Gordon Smyth's user avatar
2 votes
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Any way to quantify the variation of genes that expressed in Affymetrix expression data?

You can use the following code to calculate the coefficient of variation: ...
llrs's user avatar
  • 4,713
2 votes

What RNA-Seq expression value would be closest to Microarray equivalent?

I think it is very hard to say which are the closest because they are not really comparable. But since you are using Spearman correlation, I guess RPKM, FPKM, and TPM do not change the order of gene ...
Phoenix Mu's user avatar
2 votes

What RNA-Seq expression value would be closest to Microarray equivalent?

I did a comparison of cDNA count data against microarray data that was published a few years ago: For comparisons to published data (Fig. S2; Miller et al., 2012), a generalized linear model was ...
gringer's user avatar
  • 14.3k
2 votes

Time for running ADMIXTURE analysis

Apparently there is a bug in ADMIXTURE that prevents for converging when using at the same time the haploid mode and multithreading (flags --haploid and -j respectively). The problem is solved by ...
Iriel's user avatar
  • 31
2 votes

How to tell which channel is the reference channel in two channel (red green) array data?

No, you can't get this from the data itself. If there is a control/reference sample on one channel, you need someone to annotate which channel it's on.
user1799035's user avatar
2 votes

Different results in differential expression analysis of microarray data

DE results do not change from one run to another. The code given in your question will give identical results each time you run it.
Gordon Smyth's user avatar

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