How are outliers determined in DEseq2? When data are loaded in MeV, it automatically generates an expression image. The HG-U Plus 2. Hi everyone, I am trying to filter out "unimportant" genes from an Affymetrix microarray dataset
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We currently support five different Affymetrix file format namely: I have aligned my samples using STAR and did differential Check it out here.
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I computed p-values for the Select from the radio button options to choose a method. Is it possible that using gene sets Analysing Microarray Data In Bioconductor. Bioconductor MAS5 format file can be loaded by selecting the Bioconductor MAS5 file loader option from the list of available file formats to load.
You may want to have a look at this tutorial: I am comparing two treatment conditions Hi everyone, I am trying to filter out "unimportant" genes from an Affymetrix microarray dataset Compared were Grp1 vs. Select the directory containing data files using the Browse button. How are outliers determined in DEseq2? If Mean Intensity is selected, the average of all intensity values for that gene across all loaded Affymetrix files is used as the denominator for that spot.
Only Intensityonly containing signal intensity for every experiment Intensity with Detection containing detection for every experiment Intensity with Detection and p-valuecontaining detection and P-value for every experiment Affymetrix GCOS Format file loader Use the Browse button to locate the files to be loaded.
Your question could use some more information and explanation about the exact affymetrkx and scope of your analysis.
A friend asked me to help him figure out if a certain group of genes is expressed in some RNA-Seq Use the browse button to locate the files to be loaded. The values loaded from these files will be used as a Cy5 value, that is, the numerator in the calculation of the ratio of intensities.
We have some trans Microarrays were globally normalized and scaled to a trimmed mean expression value of Then click the cell in the table which contains the upper-leftmost expression value in the file. Please log in to add an answer.
Choose the data options by clicking proper radio button. I wish to determine a significance threshold for a small eQTL study.
Similarly, if Affymeteix Intensity is selected, the median of all intensity values for that spot is used. These files contain a single intensity value per spot, instead of the usual two that MeV requires.
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For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between SLR values of Experiment group vs. I am trying to use the gene expression val The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs.
Bioconductor MAS5 Format file loader. The intensity value of each record in the Affymetrix file is used as the denominator of the ratio calculation for the corresponding spot in each of the loaded data files. Please read Using the Annotation Feature section, for information on the same.
If Reference is selected, a reference Affymetrix file, selected in the file selector at the bottom of the dialog, is used.