Entering edit mode
hello,
i need i tab-delimited text format un which the first column is probsets, the header are array name and in between there are amounts, for example with 12 array, there are 13 colunm that the firrst is prob sets...but when i did like below, a messy file was produced that can't be used as tab-delimited and nothing is arranged alike i described
(affy)
> data <- ReadAffy()
> exp <- rma(data)
Background correcting
Normalizing
Calculating Expression
> control <- grep("AFFX",rownames(exp))
> exp <- exp[-control,]
> e <- exprs(exp)
> e <- apply(e,1,function(x) x-median(x))
> e.scaled <- t(scale(t(e),center=FALSE))
write.table(e.scaled,file="scaled.output.txt",sep="\t")
what happened please????
You have not given us enough information to go on. In addition, the code you show doesn't work anyway. As an example:
> library(affydata) > data(Dilution) > eset <- rma(Dilution) Background correcting Normalizing Calculating Expression > control <- grep("AFFX", rownames(eset)) > exp <- exp[-control,] Error in exp[-control, ] : object of type 'builtin' is not subsettableYou cannot subset an ExpressionSet the way you show in your code, so evidently that isn't what you have actually done.
At some point you have to take responsibility for what you are doing, and figure out why things went wrong. Did you check to see if e.scaled looks as you expect? Did you look at head(e.scaled)? What are the dimensions? How are you deciding that 'nothing is arranged alike i described'?
thank you Jamse, i need the codes by which in addition to RMA normalizing, i could remove control probsets (affx in prefix), median centring and set SD to 1 in per array...workbench i am working with needs a tab-delimited text format in which the column one is probsets and another column's header shows array name...BY above codes that i infered from forums, a text file was produced that columns hedear and no thing was similar to a tab-delimited format that i need and rejected by my workbench...before the above codes i used these codes:
library(affy)
> data <- ReadAffy()
> exp <- rma(data)
Background correcting
Normalizing
Calculating Expression
> control <- grep("AFFX",rownames(exp))
> exp <- exp[-control,]
> e <- exprs(exp)
> e <- apply(e,1,function(x) x-median(x))
> e.scaled <- t(scale(t(e),center=FALSE))
write.exprs(exp, file="output.txt", quote = FALSE, sep="\t", row.names=TRUE)
that produced a text output approved by workbench but i read in a forum that: just a point: you've applied changes to exp and saved it to a new variable e.scaled, so write.exprs(exp, ... ) will not reflect either centreing on the median or the scaling you've done. For your output file to reflect these changes, you will need to do something to the effect of: then i used the proposed codes that resulted a messy output and error....
in brief i totally got confused to get a codes by which i could get the proper format and reflect my median centring, SD and RMA
I HAVE 12 ARRAYS THEN I NEED 13 COLUMNS AND 33239+1 ROWS
no error i got alike the error you mentioned above
when i used these codes the header was:
library (affy)
....
data <- ReadAffy()
> exp <- rma(data)
Background correcting
Normalizing
Calculating Expression
> control <- grep("AFFX",rownames(exp))
> exp <- exp[-control,]
> e <- exprs(exp)
> e <- apply(e,1,function(x) x-median(x))
> e.scaled <- t(scale(t(e),center=FALSE))
> write.exprs(exp, file="output.txt", quote = FALSE, sep="\t", row.names=TRUE)
RPTR-Cit-CVE247372-1_at RPTR-Cit-E00696-1_s_at
GSM398930.CEL -0.42929401 0.05277762
GSM398931.CEL 0.07686754 -0.19027788
GSM398932.CEL -0.22332030 0.18392247
RPTR-Cit-ECOLOXB_at RPTR-Cit-J01347-1_s_at RPTR-Cit-J01347-2_at
GSM398930.CEL -0.1045340 0.151322706 -0.28963449
GSM398931.CEL -0.1698330 0.004327351 -0.04150183
GSM398932.CEL -0.0648303 0.061406670 0.02597463
RPTR-Cit-J01347-3_at RPTR-Cit-J01347-4_at RPTR-Cit-J01636-1_at
GSM398930.CEL 0.13856943 -0.2067401030 -0.29348645
GSM398931.CEL 0.15783703 0.0143563472 -0.06508473
GSM398932.CEL -0.05894630 0.1653155000 -0.17490760
RPTR-Cit-J01636-3_at RPTR-Cit-J01636-4_at RPTR-Cit-J03196-1_at
GSM398930.CEL 0.004818942 0.03835453 -0.01465170
GSM398931.CEL -0.080314273 0.52635794 0.08230331
GSM398932.CEL 0.003804539 -0.40785890 -0.16762973
RPTR-Cit-K01193-1_at RPTR-Cit-K01486-1_at RPTR-Cit-L36849-1_at
GSM398930.CEL -0.2325325 -0.01400262 -0.30980411
GSM398931.CEL 0.2570016 -0.45857547 0.09680378
GSM398932.CEL 0.3157111 0.31959643 -0.42947836
RPTR-Cit-M10961-1_at RPTR-Cit-M10961-2_at RPTR-Cit-M10961-4_at
GSM398930.CEL -0.23774922 -0.11077713 0.03716325
GSM398931.CEL 0.02908224 -0.13914601 -0.19691658
GSM398932.CEL -0.23597227 0.13555420 0.21130193
RPTR-Cit-M15077-1_at RPTR-Cit-M15077-1_s_at
GSM398930.CEL 0.02852942 0.49007225
GSM398931.CEL -0.25601618 -0.20245501
GSM398932.CEL -0.10846193 -0.20998255
RPTR-Cit-M57289-1_s_at RPTR-Cit-M62653-1_at
GSM398930.CEL -0.0283338 -0.280259838
GSM398931.CEL -0.5080571 -0.031315219
GSM398932.CEL -0.2153570 -0.005290923
RPTR-Cit-M62653-1_s_at RPTR-Cit-NC_001669-1_at
GSM398930.CEL 0.077976919 0.15857001
GSM398931.CEL 0.092262558 -0.08545424
GSM398932.CEL -0.032788919 -0.01906563
RPTR-Cit-NC_001669-2_at RPTR-Cit-NC_002086-1_at
GSM398930.CEL 0.001628272 -0.07071642
GSM398931.CEL -0.080531560 -0.01079547
GSM398932.CEL -0.339111833 0.14616822
RPTR-Cit-NM_131175-1_at RPTR-Cit-U43284-1_s_at
GSM398930.CEL -0.64121008 0.135687489
GSM398931.CEL 0.01962053 -0.061078966
GSM398932.CEL -0.50475198 -0.482093539
RPTR-Cit-U46493-1_s_at RPTR-Cit-U47295-1_at RPTR-Cit-U55943-1_at
GSM398930.CEL -0.09361295 -0.16202208 -0.32347980
GSM398931.CEL 0.01111139 -0.06319508 -0.31963134
GSM398932.CEL 0.23338812 -0.29688657 -0.19756045
RPTR-Cit-U57609-2_s_at RPTR-Cit-U89963-1_at
GSM398930.CEL -0.06020944 -0.4387853
GSM398931.CEL -0.13122440 0.5471873
GSM398932.CEL -0.01398634 0.1215239
RPTR-Cit-U89963-1_s_at RPTR-Cit-U89963-1_x_at
GSM398930.CEL -0.03538684 0.06096943
GSM398931.CEL -0.04355940 0.06525341
GSM398932.CEL -0.19473477 -0.01704302
RPTR-Cit-V01555-1_at RPTR-Cit-X03453-1_at RPTR-Cit-X17220-1_at
GSM398930.CEL 0.00182461 -0.268955480 0.2570698
GSM398931.CEL -0.14849961 0.029030621 0.1217726
GSM398932.CEL -0.04615403 -0.005967635 -0.1566985
RPTR-Cit-X58791-1_s_at RPTR-Cit-X58791-2_s_at
GSM398930.CEL 0.03946028 -0.353705064
GSM398931.CEL -0.15130440 0.004474927
GSM398932.CEL -0.03960688 -0.248099522
RPTR-Cit-XXU09476-1_at
GSM398930.CEL 0.006872994
GSM398931.CEL 0.254909575
GSM398932.CEL -0.282880566
[ reached getOption("max.print") -- omitted 3 rows ]
but when i used write.exprs(exp, file="output.txt", quote = FALSE, sep="\t", row.names=TRUE) instead of write.exprs(exp, file="output.txt", quote = FALSE, sep="\t", row.names=TRUE), the header was
GSM1217809_5f_02.16.07_A-1.CEL 0.05255516
GSM1217812_5f_02.16.07_F-1.CEL 0.17186324
GSM1217813_5f_02.16.07_F-2.CEL -0.13903232
RPTR-Cit-AF292559-4_s_at
GSM1217809_5f_02.16.07_A-1.CEL 0.08206178
GSM1217812_5f_02.16.07_F-1.CEL -0.40758425
GSM1217813_5f_02.16.07_F-2.CEL -0.04806016
RPTR-Cit-AF292560-1_s_at
GSM1217809_5f_02.16.07_A-1.CEL 0.002096532
GSM1217812_5f_02.16.07_F-1.CEL 0.421045649
GSM1217813_5f_02.16.07_F-2.CEL -0.017831992
RPTR-Cit-AF298789-1_at RPTR-Cit-AF323980-1_at
GSM1217809_5f_02.16.07_A-1.CEL -0.11951421 -0.27722569
GSM1217812_5f_02.16.07_F-1.CEL 0.04177827 -0.02018600
GSM1217813_5f_02.16.07_F-2.CEL -0.12014960 -0.22956421
RPTR-Cit-AF403737-1_at
GSM1217809_5f_02.16.07_A-1.CEL -0.08054451
GSM1217812_5f_02.16.07_F-1.CEL 0.15600860
GSM1217813_5f_02.16.07_F-2.CEL 0.19533998
RPTR-Cit-AJ002682-1_s_at
GSM1217809_5f_02.16.07_A-1.CEL 0.04503080
GSM1217812_5f_02.16.07_F-1.CEL -0.03033849
GSM1217813_5f_02.16.07_F-2.CEL -0.26139996
RPTR-Cit-AJ002682-2_s_at
GSM1217809_5f_02.16.07_A-1.CEL 0.2852115
GSM1217812_5f_02.16.07_F-1.CEL -0.1631590
GSM1217813_5f_02.16.07_F-2.CEL -0.0363517
RPTR-Cit-AJ132968-1_at RPTR-Cit-AY056050-1_at
GSM1217809_5f_02.16.07_A-1.CEL 0.133536388 -0.06412887
GSM1217812_5f_02.16.07_F-1.CEL 0.228111508 -0.14473409
GSM1217813_5f_02.16.07_F-2.CEL -0.194797919 -0.05747612
RPTR-Cit-AY125353_at RPTR-Cit-AY342347_at
GSM1217809_5f_02.16.07_A-1.CEL -0.1433425 -0.009057655
GSM1217812_5f_02.16.07_F-1.CEL -0.2668206 -0.014395990
GSM1217813_5f_02.16.07_F-2.CEL -0.3738729 0.056684675
RPTR-Cit-CVE247372-1_at RPTR-Cit-E00696-1_s_at
GSM1217809_5f_02.16.07_A-1.CEL 0.19075942 -0.003338260
GSM1217812_5f_02.16.07_F-1.CEL 0.24111934 0.061843554
GSM1217813_5f_02.16.07_F-2.CEL -0.08339595 -0.183964509
RPTR-Cit-ECOLOXB_at RPTR-Cit-J01347-1_s_at
GSM1217809_5f_02.16.07_A-1.CEL -0.10867961 -0.32320798
GSM1217812_5f_02.16.07_F-1.CEL 0.03054978 -0.09048522
GSM1217813_5f_02.16.07_F-2.CEL -0.21120692 -0.08085584
RPTR-Cit-J01347-2_at RPTR-Cit-J01347-3_at
GSM1217809_5f_02.16.07_A-1.CEL 0.20702548 -0.12302605
GSM1217812_5f_02.16.07_F-1.CEL -0.17961348 -0.37399036
GSM1217813_5f_02.16.07_F-2.CEL -0.14967317 0.00000000
RPTR-Cit-J01347-4_at RPTR-Cit-J01636-1_at
GSM1217809_5f_02.16.07_A-1.CEL 0.138833763 0.43868019
GSM1217812_5f_02.16.07_F-1.CEL 0.017175052 0.01354605
GSM1217813_5f_02.16.07_F-2.CEL 0.006266388 0.00000000
RPTR-Cit-J01636-3_at RPTR-Cit-J01636-4_at
GSM1217809_5f_02.16.07_A-1.CEL -0.133386582 -0.021722463
GSM1217812_5f_02.16.07_F-1.CEL 0.187753428 0.013258986
GSM1217813_5f_02.16.07_F-2.CEL -0.059438716 -0.067987479
RPTR-Cit-J03196-1_at RPTR-Cit-K01193-1_at
GSM1217809_5f_02.16.07_A-1.CEL 0.2400607 0.368636060
GSM1217812_5f_02.16.07_F-1.CEL 0.4388552 -0.069348142
GSM1217813_5f_02.16.07_F-2.CEL 0.1510561 0.037986489
RPTR-Cit-K01486-1_at RPTR-Cit-L36849-1_at
GSM1217809_5f_02.16.07_A-1.CEL 0.20840572 -0.34201316
GSM1217812_5f_02.16.07_F-1.CEL -0.07484432 0.31707235
GSM1217813_5f_02.16.07_F-2.CEL -0.15576517 0.06074941
RPTR-Cit-M10961-1_at RPTR-Cit-M10961-2_at
GSM1217809_5f_02.16.07_A-1.CEL -0.331028042 -0.12051846
GSM1217812_5f_02.16.07_F-1.CEL 0.001427136 0.00000000
GSM1217813_5f_02.16.07_F-2.CEL -0.322128415 0.08502204
RPTR-Cit-M10961-4_at RPTR-Cit-M15077-1_at
GSM1217809_5f_02.16.07_A-1.CEL -0.15341608 0.10184927
GSM1217812_5f_02.16.07_F-1.CEL -0.11565954 0.04693199
GSM1217813_5f_02.16.07_F-2.CEL -0.30116450 0.08021912
RPTR-Cit-M15077-1_s_at RPTR-Cit-M57289-1_s_at
GSM1217809_5f_02.16.07_A-1.CEL -0.08362693 0.14656191
GSM1217812_5f_02.16.07_F-1.CEL 0.08649142 -0.13507958
GSM1217813_5f_02.16.07_F-2.CEL 0.19089076 -0.09544879
RPTR-Cit-M62653-1_at RPTR-Cit-M62653-1_s_at
GSM1217809_5f_02.16.07_A-1.CEL -0.002132799 0.2219125
GSM1217812_5f_02.16.07_F-1.CEL -0.025525508 0.3162198
GSM1217813_5f_02.16.07_F-2.CEL -0.094741321 0.0000000
RPTR-Cit-NC_001669-1_at
GSM1217809_5f_02.16.07_A-1.CEL 0.35045538
GSM1217812_5f_02.16.07_F-1.CEL 0.10969333
GSM1217813_5f_02.16.07_F-2.CEL 0.13404253
RPTR-Cit-NC_001669-2_at
GSM1217809_5f_02.16.07_A-1.CEL 0.18123041
GSM1217812_5f_02.16.07_F-1.CEL -0.11793327
GSM1217813_5f_02.16.07_F-2.CEL -0.09229176
RPTR-Cit-NC_002086-1_at
GSM1217809_5f_02.16.07_A-1.CEL -0.06227755
GSM1217812_5f_02.16.07_F-1.CEL 0.01267942
GSM1217813_5f_02.16.07_F-2.CEL -0.47036044
RPTR-Cit-NM_131175-1_at RPTR-Cit-U43284-1_s_at
GSM1217809_5f_02.16.07_A-1.CEL 0.08635105 0.05726154
GSM1217812_5f_02.16.07_F-1.CEL -0.30847249 0.02293332
GSM1217813_5f_02.16.07_F-2.CEL -0.19770223 0.24267262
RPTR-Cit-U46493-1_s_at RPTR-Cit-U47295-1_at
GSM1217809_5f_02.16.07_A-1.CEL -0.14790170 -0.197104516
GSM1217812_5f_02.16.07_F-1.CEL 0.30764386 0.008246921
GSM1217813_5f_02.16.07_F-2.CEL -0.46238186 -0.056930944
RPTR-Cit-U55943-1_at RPTR-Cit-U57609-2_s_at
GSM1217809_5f_02.16.07_A-1.CEL -0.26479223 -0.70695225
GSM1217812_5f_02.16.07_F-1.CEL 0.13404993 -0.16724348
GSM1217813_5f_02.16.07_F-2.CEL -0.35250197 0.21860308
RPTR-Cit-U89963-1_at RPTR-Cit-U89963-1_s_at
GSM1217809_5f_02.16.07_A-1.CEL -0.1470777 -0.1960966
GSM1217812_5f_02.16.07_F-1.CEL 0.1693412 -0.1346432
GSM1217813_5f_02.16.07_F-2.CEL -0.2220062 -0.1183979
RPTR-Cit-U89963-1_x_at RPTR-Cit-V01555-1_at
GSM1217809_5f_02.16.07_A-1.CEL 0.16725847 0.08916747
GSM1217812_5f_02.16.07_F-1.CEL 0.07043568 0.20464053
GSM1217813_5f_02.16.07_F-2.CEL 0.06225230 -0.21173276
RPTR-Cit-X03453-1_at RPTR-Cit-X17220-1_at
GSM1217809_5f_02.16.07_A-1.CEL -0.27066087 0.4134924
GSM1217812_5f_02.16.07_F-1.CEL -0.22150327 0.0688757
GSM1217813_5f_02.16.07_F-2.CEL 0.01716142 0.0000000
RPTR-Cit-X58791-1_s_at RPTR-Cit-X58791-2_s_at
GSM1217809_5f_02.16.07_A-1.CEL 0.009855244 -0.02893986
GSM1217812_5f_02.16.07_F-1.CEL -0.098641094 -0.12332447
GSM1217813_5f_02.16.07_F-2.CEL -0.088178443 -0.28973725
RPTR-Cit-XXU09476-1_at
GSM1217809_5f_02.16.07_A-1.CEL 0.77284180
GSM1217812_5f_02.16.07_F-1.CEL 0.05441805
GSM1217813_5f_02.16.07_F-2.CEL -0.08185249
[ reached getOption("max.print") -- omitted 3 rows ]