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| | === Sanity Check === | | === Sanity Check === |
| − | Importance of Sanity Check (from [[http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae | DNA Microarray Analysis Activity]]: In summary, the p value cut-off should not be thought of as some magical number at which data becomes "significant". Instead, it is a moveable confidence level. If we want to be very confident of our data, use a small p value cut-off. If we are OK with being less confident about a gene expression change and want to include more genes in our analysis, we can use a larger p value cut-off. For the GenMAPP analysis below, we will use the fold change cut-off of greater than 0.25 or less than -0.25 and the unadjusted p value cut off of p < 0.05 for our analysis because we want to include several hundred genes in our analysis. (Note: The "AvgLogRatio" tells us the size of the gene expression change and in which direction. Positive values are increases relative to the control; negative values are decreases relative to the control. | + | Importance of Sanity Check (from [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae | DNA Microarray Analysis Activity]: In summary, the p value cut-off should not be thought of as some magical number at which data becomes "significant". Instead, it is a moveable confidence level. If we want to be very confident of our data, use a small p value cut-off. If we are OK with being less confident about a gene expression change and want to include more genes in our analysis, we can use a larger p value cut-off. For the GenMAPP analysis below, we will use the fold change cut-off of greater than 0.25 or less than -0.25 and the unadjusted p value cut off of p < 0.05 for our analysis because we want to include several hundred genes in our analysis. (Note: The "AvgLogRatio" tells us the size of the gene expression change and in which direction. Positive values are increases relative to the control; negative values are decreases relative to the control. |
| | *'''C5 and C0''' | | *'''C5 and C0''' |
| − | **How many genes have p value < 0.05? and what is the percentage (out of 5408)? | + | **''How many genes have p value < 0.05? and what is the percentage (out of 5408)?'' |
| | ***344 genes, 6.36% | | ***344 genes, 6.36% |
| − | **What about p < 0.01? and what is the percentage (out of 5408)? | + | **''What about p < 0.01? and what is the percentage (out of 5408)?'' |
| | ***94 genes, 1.74% | | ***94 genes, 1.74% |
| − | **What about p < 0.001? and what is the percentage (out of 5408)? | + | **''What about p < 0.001? and what is the percentage (out of 5408)?'' |
| | ***18 genes, 0.33% | | ***18 genes, 0.33% |
| − | **What about p < 0.0001? and what is the percentage (out of 5408)? | + | **''What about p < 0.0001? and what is the percentage (out of 5408)?'' |
| | ***5 genes, 0.09% | | ***5 genes, 0.09% |
| − | **How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 5408)? | + | **''How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 5408)?'' |
| | ***2 genes, 0.04% | | ***2 genes, 0.04% |
| − | **How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 5408)? | + | **''How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 5408)?'' |
| | ***2 genes, 0.037% | | ***2 genes, 0.037% |
| − | **Keeping the (unadjusted) "Pvalue" filter at p < 0.05, filter the "AvgLogRatio" column to show all genes with an average log fold change greater than zero. How many are there? (and %) | + | **''Keeping the (unadjusted) "Pvalue" filter at p < 0.05, filter the "AvgLogRatio" column to show all genes with an average log fold change greater than zero. How many are there? (and %)'' |
| | ***180 genes, 3.33% | | ***180 genes, 3.33% |
| − | **Keeping the (unadjusted) "Pvalue" filter at p < 0.05, filter the "AvgLogRatio" column to show all genes with an average log fold change less than zero. How many are there? (and %) | + | **''Keeping the (unadjusted) "Pvalue" filter at p < 0.05, filter the "AvgLogRatio" column to show all genes with an average log fold change less than zero. How many are there? (and %)'' |
| | ***164 genes, 3.03% | | ***164 genes, 3.03% |
| − | **What about an average log fold change of > 0.25 and p < 0.05? (and %) | + | **''What about an average log fold change of > 0.25 and p < 0.05? (and %)'' |
| | ***161 genes, 2.98% | | ***161 genes, 2.98% |
| − | **Or an average log fold change of < -0.25 and p < 0.05? (and %) (These are more realistic values for the fold change cut-offs because it represents about a 20% fold change which is about the level of detection of this technology.) | + | **''Or an average log fold change of < -0.25 and p < 0.05? (and %) (These are more realistic values for the fold change cut-offs because it represents about a 20% fold change which is about the level of detection of this technology.)'' |
| | ***149 genes, 2.76% | | ***149 genes, 2.76% |
| | *'''C20 and C0''' | | *'''C20 and C0''' |
| − | **How many genes have p value < 0.05? and what is the percentage (out of 5408)? | + | **''How many genes have p value < 0.05? and what is the percentage (out of 5408)?'' |
| | ***868 genes, 16.05% | | ***868 genes, 16.05% |
| − | **What about p < 0.01? and what is the percentage (out of 5408)? | + | **''What about p < 0.01? and what is the percentage (out of 5408)?'' |
| | ***342 genes, 6.32% | | ***342 genes, 6.32% |
| − | **What about p < 0.001? and what is the percentage (out of 5408)? | + | **''What about p < 0.001? and what is the percentage (out of 5408)?'' |
| | ***79 genes, 1.46% | | ***79 genes, 1.46% |
| − | **What about p < 0.0001? and what is the percentage (out of 5408)? | + | **''What about p < 0.0001? and what is the percentage (out of 5408)?'' |
| | ***14 genes, 0.26% | | ***14 genes, 0.26% |
| − | **How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 5408)? | + | **''How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 5408)?'' |
| | ***1 gene, 0.01% | | ***1 gene, 0.01% |
| − | **How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 5408)? | + | **''How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 5408)?'' |
| | ***34 genes, 0.63% | | ***34 genes, 0.63% |
| − | **Keeping the (unadjusted) "Pvalue" filter at p < 0.05, filter the "AvgLogRatio" column to show all genes with an average log fold change greater than zero. How many are there? (and %) | + | **''Keeping the (unadjusted) "Pvalue" filter at p < 0.05, filter the "AvgLogRatio" column to show all genes with an average log fold change greater than zero. How many are there? (and %)'' |
| | ***452 genes, | | ***452 genes, |
| − | **Keeping the (unadjusted) "Pvalue" filter at p < 0.05, filter the "AvgLogRatio" column to show all genes with an average log fold change less than zero. How many are there? (and %) | + | **''Keeping the (unadjusted) "Pvalue" filter at p < 0.05, filter the "AvgLogRatio" column to show all genes with an average log fold change less than zero. How many are there? (and %)'' |
| | ***416 genes, | | ***416 genes, |
| − | **What about an average log fold change of > 0.25 and p < 0.05? (and %) | + | **''What about an average log fold change of > 0.25 and p < 0.05? (and %)'' |
| | ***437 genes, | | ***437 genes, |
| − | **Or an average log fold change of < -0.25 and p < 0.05? (and %) (These are more realistic values for the fold change cut-offs because it represents about a 20% fold change which is about the level of detection of this technology.) | + | **''Or an average log fold change of < -0.25 and p < 0.05? (and %) (These are more realistic values for the fold change cut-offs because it represents about a 20% fold change which is about the level of detection of this technology.)'' |
| | ***405 genes, | | ***405 genes, |
| | *'''C60 and C0''' | | *'''C60 and C0''' |
| − | **How many genes have p value < 0.05? and what is the percentage (out of 5408)? | + | **''How many genes have p value < 0.05? and what is the percentage (out of 5408)?'' |
| | ***1017 genes, 18.81% | | ***1017 genes, 18.81% |
| − | **What about p < 0.01? and what is the percentage (out of 5408)? | + | **''What about p < 0.01? and what is the percentage (out of 5408)?'' |
| | ***471 genes, 8.71% | | ***471 genes, 8.71% |
| − | **What about p < 0.001? and what is the percentage (out of 5408)? | + | **''What about p < 0.001? and what is the percentage (out of 5408)?'' |
| | ***163 genes, 3.01% | | ***163 genes, 3.01% |
| − | **What about p < 0.0001? and what is the percentage (out of 5408)? | + | **''What about p < 0.0001? and what is the percentage (out of 5408)?'' |
| | ***53 genes, 0.98% | | ***53 genes, 0.98% |
| − | **How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 5408)? | + | **''How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 5408)?'' |
| | ***13 genes, 0.24% | | ***13 genes, 0.24% |
| − | **How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 5408)? | + | **''How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 5408)?'' |
| | ***229 genes, 4.23% | | ***229 genes, 4.23% |
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#5 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(980): MappedDiff->__construct()
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