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What software is available for analyzing the results from my human, mouse, or rat transcriptome assays? Product FAQ

Answer

Probe cell intensity data (CEL) from human, mouse, or rat transcriptome assays are analyzed in Transcriptome Analysis Console(TAC) Software. The application uses a version of RMA analysis to create CHP files. Transcriptome Analysis  Console Software can be downloaded at no charge from the website. Further statistical analysis may be performed in Affymetrix' Transcriptome Analysis Console (TAC) Software to obtain a list of differentially expressed genes and alternative splicing events. TAC Software also provides the visualization of genes, exons, junctions, transcript isoforms, pathways, and mRNA-miRNA regulatory networks.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Answer Id: E14108

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What data analysis software solutions are offered? Product FAQ

Answer

We provideTranscriptome Analysis Console Software for normalization, summarization,  differential expression analysis and visualization free of charge. Due to the presence of multiple organisms on the miRNA arrays, the chromosomal location feature in Transcriptome Analysis Console Software will not give accurate results.

For analysis in Transcriptome Analysis Console Software, array type-specific configuration and annotation files are required. Use the “Download Array Type Files” button in the Preferences tab to download and install array type-specific library files.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Answer Id: E14130

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For miRNA array plates, what microarray data analysis software solutions are offered? Product FAQ

Answer

The CEL files generated from this array is compatible with  Transcriptome Analysis Console and can be used for normalization, signal summarization and differential expression analysis of your experimental data.

For analysis in Transcriptome Analysis Console Software, array type specific configuration and annotation files are required. Use the “Download Array Type Files” button in the Preferences tab to download and install array type specific library files.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Answer Id: E14114

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Is the Transcriptome Analysis Console (TAC) tool freely available? Product FAQ

Answer

Yes, the TAC tool is available for free. It can be downloaded from this link (https://downloads.thermofisher.com/TAC/TAC_4.0.2/TAC4x64.exe).

Answer Id: E13071

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What data analysis software solutions are offered for QuantiGene Plex assays? Product FAQ

Answer

The QuantiGene data analysis app is available on the Thermo Fisher Connect Platform for analyzing QuantiGene Plex assay data. For advanced QuantiGene Plex assay data analysis and visualization, the free desktop application software, Applied Biosystems Transcriptome Analysis Console (TAC) software can be used.

Answer Id: E19631

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What are the input files for the Transcriptome Analysis Console (TAC)? Product FAQ

Answer

The TAC needs expression data in .chp file format. The Oncomine Immune Response Research Plugin automatically generates these .chp formatted files. In addition, the TAC needs to be configured for analysis of the Oncomine Immune Response Research Assay data with these two files: the Transcripts Annotation file (https://s3.amazonaws.com/IonTorrent/usbupdate/TAC_4.0/Immune-response.transcript.csv) and TAC Analysis Parameters file (https://s3.amazonaws.com/IonTorrent/usbupdate/TAC_4.0/Immune-response.TAC_ARRAY_CONFIG). Your local support specialist can provide the bed file for the panel.

Answer Id: E13073

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Which algorithm do I use to run the analysis for these new HT PM Plate Arrays? Product FAQ

Answer

We recommend running the RMA algorithm in the Transcriptome Analysis Console (TAC).

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Answer Id: E13603

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Transcriptome Analysis Console 4.0 Release Notes Product Literature

What are the input files for the Transcriptome Analysis Console (TAC) for Ion Ampliseq Transcriptome Human Gene Expression Kit? Product FAQ

Answer

The TAC needs expression data in .chp file format. The ampliseqRNA analysis Plugin automatically generates these .chp formatted files. In addition, the TAC needs to be configured for analysis of the Ion AmpliSeq Transcriptome Human Gene Expression data with these two files: the Transcripts Annotation file (https://s3.amazonaws.com/IonTorrent/usbupdate/TAC_4.0/hg19_AmpliSeq_Transcriptome_21K_v1.transcript.csv) and TAC Analysis Parameters file (https://s3.amazonaws.com/IonTorrent/usbupdate/TAC_4.0/hg19_AmpliSeq_Transcriptome_21K_v1.tac_array_config). Your local support specialist can provide the bed file for the panel.

Answer Id: E15977

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What are the input files for the Transcriptome Analysis Console (TAC) for Ion Ampliseq Transcriptome Mouse Gene Expression Kit? Product FAQ

Answer

The TAC needs expression data in .chp file format. The ampliseqRNA analysis Plugin automatically generates these .chp formatted files. In addition, the TAC needs to be configured for analysis of the Ion AmpliSeq Transcriptome Mouse Gene Expression data with these two files: the Transcripts Annotation file (https://s3.amazonaws.com/IonTorrent/usbupdate/TAC_4.0/AmpliSeq_Mouse_Transcriptome_V1_Designed.transcript.csv) and TAC Analysis Parameters file (https://s3.amazonaws.com/IonTorrent/usbupdate/TAC_4.0/AmpliSeq_Mouse_Transcriptome_V1_Designed.TAC_ARRAY_CONFIG). Your local support specialist can provide the bed file for the panel.

Answer Id: E15976

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Why am I unable to visualize certain parts of the wikipathways in the Transcriptome Analysis Console (TAC) software? Product FAQ

Answer

The TAC currently does not provide pathway analysis for small panels such as the Oncomine Immune Response Research Assay.

Answer Id: E13074

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User Guide: Transcriptome Analysis Console (TAC) 4.0 Manual / Product Insert

  • Version: 8
Catalog #

Which of the gene arrays are compatible with the miRNA interaction network in Transcriptome Analysis Console (TAC) Software? Product FAQ

Answer

The miRNA interaction network in TAC Software is available for all gene arrays, including model organisms. To have the interaction network available, the same samples must have been processed through both the gene array and the miRNA array. Additionally, the gene array being used must have a gene symbol column displayed in their annotation.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Answer Id: E18712

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Transcriptome Analysis Console Software 3.1 Release Notes Product Literature

What does FDR refer to in the Transcriptome Analysis Console (TAC) Software analysis output/result tables? Product FAQ

Answer

FDR, or False Discovery Rate, is a statistical method used in multiple hypothesis testing to correct for multiple comparisons. The FDR is controlled at a certain alpha level (default 0.05 in all result tables). This means that the expected proportion of rejections that are in error is less than the alpha level. Alpha level can be customized in the TAC result tables by changing the default filtering criteria in the FDR p-value column (0.05) to a different value.
Please refer to the following publication for further details on the algorithm: Benjamini, Yoav; Hochberg, Yosef (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B (Methodological) 57 (1): 289-300. MR 1325392.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Answer Id: E18723

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