CARMAweb protocols

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chevron_left Gene expression classification Gene expression clustering Gene expression microarray data visualization Bioinformatics workflows Differential expression detection Normalization Normalization Data preprocessing Over-representation analysis chevron_right
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CARMAweb specifications

Information


Unique identifier OMICS_14345
Name CARMAweb
Alternative name Comprehensive R-based Microarray Analysis web service
Interface Web user interface
Restrictions to use None
Output data An RData file.
Programming languages Java
Computer skills Basic
Version 1.6
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Zlatko Trajanoski <>

Publication for Comprehensive R-based Microarray Analysis web service

CARMAweb in pipelines

 (4)
2017
PMCID: 5551015
PMID: 28793908
DOI: 10.1186/s12931-017-0629-3

[…] group means. p < 0.05 was considered as significant in all cases. for microarray data, statistical analyses were performed by utilizing the statistical programming environment r [] implemented in carmaweb []. genewise testing for differential expression used t-test and benjamini-hochberg multiple testing correction [false discovery rate (fdr) ≤ 0.10]. gene ontology (go) term and pathway […]

2015
PMCID: 4525140
PMID: 26243655
DOI: 10.1038/srep12673

[…] or one way anova with dunnett’s multiple comparison test. for microarray experiments statistical analyses were performed by utilizing the statistical programming environment r implemented in carmaweb. genewise testing for differential expression was done employing limma t-test and benjamini-hochberg multiple testing correction (fdr < 10%). right-tailed fisher exact test was utilized […]

2015
PMCID: 4731435
PMID: 26662513
DOI: 10.1007/s00335-015-9616-5

[…] settings including median polish and sketch-quantile normalization). statistical analyses were performed by utilizing the statistical programming environment r (r core team ) implemented in carmaweb (rainer et al. ). genewise testing for differential expression was done employing the limma t test and benjamini-hochberg multiple testing correction (fdr < 10 %). the cluster dendrogram […]

2009
PMCID: 2730013
PMID: 19718442
DOI: 10.1371/journal.pone.0006838

[…] background effects, within-array variation and between-array variation, we normalized the signal intensity of the two dye channels using the three-step procedure described by and implemented in carmaweb . in short, the relative expression level and probability of differential expression between infected and uninfected flies for each gene was estimated using the markov chain monte carlo […]


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CARMAweb in publications

 (49)
PMCID: 5953988
PMID: 29765129
DOI: 10.1038/s41598-018-25762-5

[…] redundant probe sets with identical expression values in all samples were removed from the dataset. statistical analyses were performed using the statistical programming environment implemented in carmaweb. gene wise testing for differential expression was done employing the (limma) t-test and benjamini-hochberg multiple testing correction (fdr < 10%). sets of significantly regulated mirnas […]

PMCID: 5925963
PMID: 29740265
DOI: 10.3389/fnins.2018.00220

[…] and were therefore excluded in this analysis in order to minimize any false positives. datasets were processed for robust multi-array average (rma) normalization on carma software suite (https://carmaweb.genome.tugraz.at/carma/) comprehensive r- and bioconductor-based web service for microarray data analysis (rainer et al., ), and additionally via r/bioconductor using standard procedures. […]

PMCID: 5880583
PMID: 28901330
DOI: 10.1038/ijo.2017.224

[…] define sets of enriched canonical pathways (p<0.05) or biological functions (p<0.01). statistical analyses were performed by utilizing the statistical programming environment r, implemented in carmaweb (carmaweb version 1.5.18—uses r version 2.11.0 together with bioconductor version 2.6), graphpad prism 6 and spss version 22., to investigate molecular alterations caused by a history […]

PMCID: 5666744
PMID: 28953266
DOI: 10.3390/ijms18102062

[…] were scanned using a genechip scanner 3000 7g (thermo fisher scientific) and command console software v. 3.2.3 (thermo fisher scientific) to produce. cel intensity files which were processed with carmaweb (comprehensive r-based microarray analysis web service). genespring software (agilent, santa clara, ca, usa) was used to perform statistical analysis. specifically, samples were first […]

PMCID: 5443495
PMID: 28542224
DOI: 10.1371/journal.pone.0174174

[…] type-signal and detection p value; background-perfect match gc composition-based background correction (pm-gcbg); normalization method-sketch-quantile., gene expression data were then processed via carmaweb (comprehensive r based microarray analysis web service) using the significance analysis of microarrays (sam) method to get fold changes for determining differential expression and p values. […]


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CARMAweb institution(s)
Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria; Christian-Doppler Laboratory for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria; Tyrolean Cancer Research Institute, Innsbruck, Austria
CARMAweb funding source(s)
This work was supported by the bm:bwk project GEN-AU BIN (Bioinformatic Integration Network) and the Tyrolean Cancer Research Institute.

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