test RUVSeq

countTable_UTRPolysomes_ERCC_21Nov2017.txt

-ERCC	2and3Hc2_R1.MACE.cleaned	2and3Hc3_R1.MACE.cleaned	4and5Hc2_R1.MACE.cleaned	4and5Hc3_R1.MACE.cleaned	6and7Hc2_R1.MACE.cleaned	6and7Hc3_R1.MACE.cleaned	80SHc2_R1.MACE.cleaned	80SHc3_R1.MACE.cleaned	InputHc2_R1.MACE.cleaned	InputHc3_R1.MACE.cleaned	bigger7Hc2_R1.MACE.cleaned	bigger7Hc3_R1.MACE.cleaned
+ERCC	2and3Hc2	2and3Hc3	4and5Hc2	4and5Hc3	6and7Hc2	6and7Hc3	80SHc2	80SHc3	InputHc2	InputHc3	bigger7Hc2	bigger7Hc3
 ERCC-00002	9140	12382	15199	9748	11895	9531	3575	6079	31329	26857	26377	9934
 ERCC-00003	382	456	632	280	374	300	106	152	1438	1280	957	233
 ERCC-00004	3920	4865	6757	3681	4579	3910	1274	1961	13739	11403	11893	3558

countTable_UTRPolysomes_Stats_21Nov2017.txt

 sample	reads.raw	reads.aligned	reads.ercc	reads.mito	ratio.aligned	ratio.ercc	ratio.mito
-2and3Hc2_R1.MACE.cleaned	6502897	5124752	58939	53339	78.807215	0.906350	0.820234
-2and3Hc3_R1.MACE.cleaned	7693990	6060973	74730	50336	78.775421	0.971278	0.654225
-4and5Hc2_R1.MACE.cleaned	9086127	7244897	101015	34267	79.735810	1.111750	0.377135
-4and5Hc3_R1.MACE.cleaned	5901348	4706567	59028	14532	79.754100	1.000246	0.246249
-6and7Hc2_R1.MACE.cleaned	4771834	3862606	72877	12133	80.945942	1.527233	0.254263
-6and7Hc3_R1.MACE.cleaned	4655716	3758648	58274	8124	80.731900	1.251666	0.174495
-80SHc2_R1.MACE.cleaned	1163641	822494	20707	41857	70.682796	1.779501	3.597072
-80SHc3_R1.MACE.cleaned	1629758	1101244	33667	53700	67.571014	2.065767	3.294968
-InputHc2_R1.MACE.cleaned	5831777	4305878	204928	101238	73.834751	3.513989	1.735972
-InputHc3_R1.MACE.cleaned	4824334	3422604	173967	55973	70.944590	3.606031	1.160222
-bigger7Hc2_R1.MACE.cleaned	10560307	8716563	194216	19836	82.540811	1.839113	0.187835
-bigger7Hc3_R1.MACE.cleaned	3646327	2993304	60957	6142	82.090937	1.671737	0.168443
+2and3Hc2	6502897	5124752	58939	53339	78.807215	0.906350	0.820234
+2and3Hc3	7693990	6060973	74730	50336	78.775421	0.971278	0.654225
+4and5Hc2	9086127	7244897	101015	34267	79.735810	1.111750	0.377135
+4and5Hc3	5901348	4706567	59028	14532	79.754100	1.000246	0.246249
+6and7Hc2	4771834	3862606	72877	12133	80.945942	1.527233	0.254263
+6and7Hc3	4655716	3758648	58274	8124	80.731900	1.251666	0.174495
+80SHc2	1163641	822494	20707	41857	70.682796	1.779501	3.597072
+80SHc3	1629758	1101244	33667	53700	67.571014	2.065767	3.294968
+InputHc2	5831777	4305878	204928	101238	73.834751	3.513989	1.735972
+InputHc3	4824334	3422604	173967	55973	70.944590	3.606031	1.160222
+bigger7Hc2	10560307	8716563	194216	19836	82.540811	1.839113	0.187835
+bigger7Hc3	3646327	2993304	60957	6142	82.090937	1.671737	0.168443

edgeR_RUVSeqNorm.R

+#edgeR_RUVSeq
+#
+# RUVSeq 
+#
+# georgi.tushev@brain.mpg.de
+# Nov 2017
+
+# load edgeR
+library(edgeR);
+library(RUVSeq);
+
+# clean current variables
+rm(list = ls());
+
+# read counts
+indata<-as.matrix(read.table("/Users/tushevg/Desktop/UTRPolyribosomes/countTable_UTRPolysomes_ERCC_21Nov2017.txt",stringsAsFactors=F, header=T, row.names=1));
+
+
+

polyribosomeAnalysis.m

@@ -26,3 +26,5 @@ data.window = txt{4};
 data.span = txt{5};
 data.reads = txt{6};
 data.counts = [txt{7:end}];
+
+