Splicing in a Cancer Gene

The CVC group

June 13, 2013

First Slide

Array data: Probes to Probesets to Genes to samples to groups geo_accession, ALL cancer type, Probe, Perfect Match Signal

stuff

Probe Level Expression

MyAffyData<-read.csv("217422_s_at_probes_PMsignal_stacked.csv", header = TRUE)
head(MyAffyData)

  geo_accession       characteristics_ch1                        Probe  PM
1     GSM329407 mature B-ALL with t(8;14) HG-U133_PLUS_2:217422_S_AT_2 126
2     GSM329407 mature B-ALL with t(8;14) HG-U133_PLUS_2:217422_S_AT_3  97
3     GSM329407 mature B-ALL with t(8;14) HG-U133_PLUS_2:217422_S_AT_4  87
4     GSM329407 mature B-ALL with t(8;14) HG-U133_PLUS_2:217422_S_AT_5 145
5     GSM329407 mature B-ALL with t(8;14) HG-U133_PLUS_2:217422_S_AT_6 137
6     GSM329407 mature B-ALL with t(8;14) HG-U133_PLUS_2:217422_S_AT_7 197

Exon 12 probes PM signal

Exon12<-subset(MyAffyData,Probe=="HG-U133_PLUS_2:217422_S_AT_5")
bwplot(characteristics_ch1~PM, data=Exon12)

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Exon12_B<-subset(MyAffyData,Probe=="HG-U133_PLUS_2:217422_S_AT_6")
bwplot(characteristics_ch1~PM, data=Exon12_B)

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Exon 12 Log PM signal

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Exon14

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