13
votes
Accepted
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 ...
- 19.6k
9
votes
Accepted
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 ...
- 646
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, ...
- 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 ...
- 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 ...
- 191
6
votes
Accepted
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 (...
- 397
6
votes
Accepted
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 ...
- 4,693
5
votes
Accepted
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 ...
- 19.6k
5
votes
Accepted
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 ...
- 827
3
votes
Accepted
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 ...
- 1,012
3
votes
Accepted
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.
...
- 629
3
votes
Accepted
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 ...
- 3,571
3
votes
Accepted
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 ...
- 19.6k
3
votes
Accepted
Calculating mean accross rows with repeated entries in R
Using group_by from dplyr
You can use group_by function from ...
- 1,021
3
votes
Accepted
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 ...
- 118
2
votes
Accepted
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 ...
- 435
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 ...
- 13.8k
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 ...
- 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 ...
- 4,693
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 ...
- 4,693
2
votes
Accepted
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 (...
- 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 ...
- 2,676
2
votes
Accepted
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 ...
- 19.6k
2
votes
Accepted
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 <...
- 281
2
votes
Accepted
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:
...
- 4,693
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 ...
- 857
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 ...
- 13.8k
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 ...
- 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.
- 118
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.
- 281
Only top scored, non community-wiki answers of a minimum length are eligible