gravatar for bjwiley23

2 hours ago by

Hi,
I have below code to summarize the exon and gene intensities. I am wondering why for 1 gene it has the same values (logged) as one of the probes so that when doing Gene-level Normalized intensity subtracting (since its logged) I'll get 0 for each sample. How is this the case that gene level intensity returned from APT is same as an exon?

#gene estimates (exon array)
apt-probeset-summarize 
-p /software/apt/lib/HuEx-1_0-st-v2.r2.pgf 
-c /software/apt/lib/HuEx-1_0-st-v2.r2.clf 
-b /software/apt/lib/HuEx-1_0-st-v2.r2.antigenomic.bgp 
--qc-probesets /software/apt/lib/HuEx-1_0-st-v2.r2.qcc 
-m /software/apt/lib/HuEx-1_0-st-v2.r2.dt1.hg18.core.mps 
-a rma-sketch 
--kill-list /software/apt/lib/Affymetrix_HuEx_1.0ST_Affected_probes_probesets.txt 
-o output-dir/gene 
/cels/exon/keep/*.CEL

#exon estimates (exon array)
apt-probeset-summarize 
-p /software/apt/lib/HuEx-1_0-st-v2.r2.pgf 
-c /software/apt/lib/HuEx-1_0-st-v2.r2.clf 
-b /software/apt/lib/HuEx-1_0-st-v2.r2.antigenomic.bgp 
--qc-probesets /software/apt/lib/HuEx-1_0-st-v2.r2.qcc 
-s /software/apt/lib/HuEx-1_0-st-v2.r2.dt1.hg18.core.ps 
-a rma-sketch 
--kill-list /software/apt/lib/Affymetrix_HuEx_1.0ST_Affected_probes_probesets.txt 
-o output-dir/exon 
/cels/exon/keep/*.CEL

An example is transcript_cluster_id 2315918

grep 2315918 rma-sketch.summary.txt
2315918 6.42343 6.51861 6.41761 6.48735 5.99480 6.52973 6.05458 6.88223 7.26753 6.37890

And one of the exons 2315941

grep 2315941 rma-sketch.summary.txt
2315941 6.42343 6.51861 6.41761 6.48735 5.99480 6.52973 6.05458 6.88223 7.26753 6.37890

This happened for more than 1 study too so is it specific to a particular gene? This is for NM_001039211 // ATAD3C, exon id 439.



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