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karthik3k
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Why do we use two channels in MICRO ARRAY analysis ??
LIke red and Green ??
What does the ratio between red/green signify ??
LIke red and Green ??
What does the ratio between red/green signify ??
It all depends on what you are doing, but generally when you amplify RNA you loose the 5' end of the transcript, that has to do with the way the primers anneal. For the 3' end you can make a primer with a poly-A tail, so you will always amplify the end. For the 5' end there is no common tail for all the different gene-transcripts, so a random primer is used. That primer can anneal anywhere in the transcript so you never know how full length your cDNA is. That is why there is a bias towards the 3', it depends how efficiently the amplification procedure went, whether there are long amplicons.Before selecting individual probes from either exemplars or consensus sequences, the 5' to 3' orientation of each transcript must be determined. Affymetrix uses computer algorithms that combine information from public annotations with in-house identification of splice signals, polyadenylation sites, and polyadenylation signals to distinguish sense from antisense strands. If the orientation cannot be determined unequivocally due to contradictory information, then the probes for both strands are generated.
In general, 11 to16 probes are selected among all possible 25-mers to represent each transcript. In addition to choosing the probes based on their predicted hybridization properties, candidate sequences are filtered for specificity. Their potential for cross-hybridizing with similar, but unrelated sequences, is evaluated.
To obtain a complete picture of a gene's activity, some probes are selected from regions shared by multiple splice or polyadenylation variants. In other cases, unique probes that distinguish between variants are favored. Inter-probe distance is also factored into the selection process. Probes are 3'-biased to match the target generation characteristics of our sample amplification method, but they are also widely spaced to sample various regions of each transcript and provide robustness of detection.
Predictors are differentially expressed genes that correlate with the phenotype.
Karthik3k, we need you to clarify what you are doing! :)karthik3k said:What are Predictors ?
How do i find them in Micro array clusters ??
Microarray analysis is a technique used to measure the expression levels of thousands of genes simultaneously. Two channels are used in this technique because they allow for the comparison of gene expression levels between two different samples. By labeling each sample with a different fluorescent dye, we can detect and compare the levels of gene expression in both samples simultaneously.
The two channels in microarray analysis represent two different samples. One sample is labeled with a red fluorescent dye, while the other is labeled with a green fluorescent dye. This allows us to differentiate between the two samples and compare the levels of gene expression.
Yes, it is possible to use more than two channels in microarray analysis. This is known as multi-channel microarray analysis and allows for the comparison of gene expression levels between more than two samples. However, using more than two channels can be more complex and may require more advanced analysis techniques.
The two channels in microarray analysis enable us to compare the expression levels of genes between two samples. By detecting the differences in gene expression between the two channels, we can identify which genes are differentially expressed, or have significantly different levels of expression between the two samples.
There is no specific order in which the two channels should be analyzed in microarray analysis. Both channels should be analyzed simultaneously to compare the expression levels of genes between the two samples. However, it is important to ensure that the labeling of the samples with the fluorescent dyes is accurate and consistent to obtain reliable results.