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Search results for the GEO ID: GSE5348
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GSM ID
GPL ID
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Title
Source name
Description
Characteristics
GSM121547
GPL339
liver, ATP7B KO mouse, sample KO903 liver RNA, ATP 7B KO mouse (first described Hum. Mol. Genet. (1999) 8:1665-1671) ATP7B -/- Ko mice, 6 weeks old *Data analysis. *The array image scan is processed with Affymetrix Microarray Suite, version 5.0 (MAS 5.0) software. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS, six values are examined to assess overall assay performance: background, noise, average Signal, % Present, ratio of Signal values for probe sets representing the 5’ and 3’ ends of actin and GAPDH transcripts, and total Signal for probe sets for BioC, BioD and CreX. Assays demonstrating poor or marginal performance are flagged. An MAS 5.0 absolute expression analysis was performed for each GeneChip genome array hybridization. Following the initial analysis, the absolute analyses were rerun using global scaling to an average target intensity of */350/*. The scaling allows for the direct comparison of hybridization values from the different targets analyzed in this project (and with any additional GeneChip sample assays you run using the same array type). For each analysis, scaled or unscaled, the parameters a_1 and a_2 are set to 0.1 and 0.15 respectively. These parameters set the point at which a probeset is called present(P), marginal(M), or undetectable(A). This call is based on the Detection p-value of the probeset.
GSM121550
GPL339
liver, ATP7B KO mouse, sample KO904 liver RNA, ATP 7B KO mouse (first described Hum. Mol. Genet. (1999) 8:1665-1671) ATP7B -/- KO mice, 6 weeks old *Data analysis. *The array image scan is processed with Affymetrix Microarray Suite, version 5.0 (MAS 5.0) software. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS, six values are examined to assess overall assay performance: background, noise, average Signal, % Present, ratio of Signal values for probe sets representing the 5' and 3' ends of actin and GAPDH transcripts, and total Signal for probe sets for BioC, BioD and CreX. Assays demonstrating poor or marginal performance are flagged. An MAS 5.0 absolute expression analysis was performed for each GeneChip genome array hybridization. Following the initial analysis, the absolute analyses were rerun using global scaling to an average target intensity of */350/*. The scaling allows for the direct comparison of hybridization values from the different targets analyzed in this project (and with any additional GeneChip sample assays you run using the same array type). For each analysis, scaled or unscaled, the parameters a_1 and a_2 are set to 0.1 and 0.15 respectively. These parameters set the point at which a probeset is called present(P), marginal(M), or undetectable(A). This call is based on the Detection p-value of the probeset.
GSM121552
GPL339
liver, ATP7B KO mouse, sample KO905 liver RNA, ATP 7B KO mouse (first described Hum. Mol. Genet. (1999) 8:1665-1671) ATP7B -/- Ko mice, 6 weeks old *Data analysis. *The array image scan is processed with Affymetrix Microarray Suite, version 5.0 (MAS 5.0) software. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS, six values are examined to assess overall assay performance: background, noise, average Signal, % Present, ratio of Signal values for probe sets representing the 5' and 3' ends of actin and GAPDH transcripts, and total Signal for probe sets for BioC, BioD and CreX. Assays demonstrating poor or marginal performance are flagged. An MAS 5.0 absolute expression analysis was performed for each GeneChip genome array hybridization. Following the initial analysis, the absolute analyses were rerun using global scaling to an average target intensity of */350/*. The scaling allows for the direct comparison of hybridization values from the different targets analyzed in this project (and with any additional GeneChip sample assays you run using the same array type). For each analysis, scaled or unscaled, the parameters a_1 and a_2 are set to 0.1 and 0.15 respectively. These parameters set the point at which a probeset is called present(P), marginal(M), or undetectable(A). This call is based on the Detection p-value of the probeset.
GSM121554
GPL339
liver, wt mouse, sample WT4 liver RNA, wt mouse 6 weeks old *Data analysis. *The array image scan is processed with Affymetrix Microarray Suite, version 5.0 (MAS 5.0) software. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS, six values are examined to assess overall assay performance: background, noise, average Signal, % Present, ratio of Signal values for probe sets representing the 5' and 3' ends of actin and GAPDH transcripts, and total Signal for probe sets for BioC, BioD and CreX. Assays demonstrating poor or marginal performance are flagged. An MAS 5.0 absolute expression analysis was performed for each GeneChip genome array hybridization. Following the initial analysis, the absolute analyses were rerun using global scaling to an average target intensity of */350/*. The scaling allows for the direct comparison of hybridization values from the different targets analyzed in this project (and with any additional GeneChip sample assays you run using the same array type). For each analysis, scaled or unscaled, the parameters a_1 and a_2 are set to 0.1 and 0.15 respectively. These parameters set the point at which a probeset is called present(P), marginal(M), or undetectable(A). This call is based on the Detection p-value of the probeset.
GSM121555
GPL339
liver, wt mouse, sample WT5 liver RNA, WT mouse 6 weeks old *Data analysis. *The array image scan is processed with Affymetrix Microarray Suite, version 5.0 (MAS 5.0) software. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS, six values are examined to assess overall assay performance: background, noise, average Signal, % Present, ratio of Signal values for probe sets representing the 5' and 3' ends of actin and GAPDH transcripts, and total Signal for probe sets for BioC, BioD and CreX. Assays demonstrating poor or marginal performance are flagged. An MAS 5.0 absolute expression analysis was performed for each GeneChip genome array hybridization. Following the initial analysis, the absolute analyses were rerun using global scaling to an average target intensity of */350/*. The scaling allows for the direct comparison of hybridization values from the different targets analyzed in this project (and with any additional GeneChip sample assays you run using the same array type). For each analysis, scaled or unscaled, the parameters a_1 and a_2 are set to 0.1 and 0.15 respectively. These parameters set the point at which a probeset is called present(P), marginal(M), or undetectable(A). This call is based on the Detection p-value of the probeset.
GSM121556
GPL339
liver, WT mouse, sample WT6 Liver RNA, WT mice WT mice, 6 weeks old *Data analysis. *The array image scan is processed with Affymetrix Microarray Suite, version 5.0 (MAS 5.0) software. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS, six values are examined to assess overall assay performance: background, noise, average Signal, % Present, ratio of Signal values for probe sets representing the 5' and 3' ends of actin and GAPDH transcripts, and total Signal for probe sets for BioC, BioD and CreX. Assays demonstrating poor or marginal performance are flagged. An MAS 5.0 absolute expression analysis was performed for each GeneChip genome array hybridization. Following the initial analysis, the absolute analyses were rerun using global scaling to an average target intensity of */350/*. The scaling allows for the direct comparison of hybridization values from the different targets analyzed in this project (and with any additional GeneChip sample assays you run using the same array type). For each analysis, scaled or unscaled, the parameters a_1 and a_2 are set to 0.1 and 0.15 respectively. These parameters set the point at which a probeset is called present(P), marginal(M), or undetectable(A). This call is based on the Detection p-value of the probeset.
 
 
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