[BioC] [R] help with linear model
Ista Zahn
istazahn at gmail.com
Mon Oct 26 11:23:23 CET 2009
I'm not familiar with microarray data, so I hope I'm not off base here.
Data frames are structured so that variables appear in the columns and
cases in the rows. From your formula it looks like you're trying to
fit a model using rows as variables and columns as cases. There is
probably a way to do this, but It might be easier to just flip your
data. One way to do this is
dataNew <- as.data.frame(t(data))
row.names(dataNew) <- names(data)
names(dataNew) <- paste("I",row.names(data), sep="") #variable names
should start with a letter
(note that naming your data "data" is not a good practice.)
Now you should be able to run your model as before (prefixing "I" to
the variable names to match the new naming scheme):
m1 = lm(norm ~ I206427_s_at + I205338_s_at + I209848_s_at + I205694_at
+ I201909_at + I208894_at + I216512_s_at + I205337_at + I201850_at +
I210982_s_at, data=dataNew)
Hope it helps,
Ista
On Mon, Oct 26, 2009 at 5:48 AM, Eleni Christodoulou
<elenichri at gmail.com> wrote:
> Dear list,
>
> I have been searching for a week to fit a simple linear model to my data. I
> have looked into the previous posts but I haven't found anything relevant to
> my problem. I guess it is something simple...I just cannot see it.
> I have the following data frame, named "data", which is a subset of a
> microarray experiment. The columns are the samples and the rows are the
> probes. I binded the first line, called "norm", which represents the
> estimated output. I want to create a linear model which shows the
> relationship between the gene expressions (rows) and the output (norm).
>
> *data*
> GSM276723.CEL GSM276724.CEL GSM276725.CEL GSM276726.CEL
> norm 0.897000 0.590000 0.683000 0.949000
> 206427_s_at 5.387205 6.036506 8.824783 10.864122
> 205338_s_at 6.454779 13.143095 6.123212 12.726562
> 209848_s_at 6.703062 7.783330 12.175654 9.339651
> 205694_at 5.894131 5.794516 12.876555 11.534664
> 201909_at 12.616538 12.913255 12.275182 12.767743
> 208894_at 13.049286 9.317874 12.873516 13.527182
> 216512_s_at 6.324789 12.783791 6.216932 12.013404
> 205337_at 6.175940 12.158796 6.117519 12.041078
> 201850_at 6.633013 6.465900 6.535434 7.749985
> 210982_s_at 12.444791 8.597388 12.197696 12.963449
> GSM276727.CEL GSM276728.CEL GSM276729.CEL GSM276731.CEL
> norm 0.302000 0.597000 0.270000 0.530000
> 206427_s_at 5.690357 8.014055 13.034753 5.493977
> 205338_s_at 5.757048 7.706341 13.258410 5.562588
> 209848_s_at 6.461028 7.036515 13.633649 5.874098
> 205694_at 5.519552 5.297107 6.498811 5.146150
> 201909_at 12.814454 11.592632 6.594229 6.650796
> 208894_at 13.835359 13.028096 5.839909 6.045578
> 216512_s_at 6.033096 7.273650 12.669054 5.946932
> 205337_at 5.879028 7.381713 12.633829 5.379559
> 201850_at 9.684397 6.560014 8.523229 6.573052
> 210982_s_at 13.342729 12.470517 5.903681 5.658115
> GSM276732.CEL GSM276735.CEL GSM276736.CEL GSM276737.CEL
> norm 0.43400 0.647000 0.113000 1.000000
> 206427_s_at 12.80257 5.645002 6.519554 13.572480
> 205338_s_at 13.38057 5.804107 11.090690 14.024922
> 209848_s_at 13.27718 6.490851 9.784199 14.101162
> 205694_at 11.37717 5.802105 7.944963 14.060492
> 201909_at 13.24126 12.263899 12.578315 6.443491
> 208894_at 12.29916 7.563361 9.971493 7.094214
> 216512_s_at 13.00303 5.905789 10.512761 13.647573
> 205337_at 12.63560 5.430138 10.707242 13.020312
> 201850_at 12.71874 6.275480 6.987962 12.354580
> 210982_s_at 11.53559 7.225199 9.322706 6.617615
> GSM276738.CEL GSM276739.CEL GSM276740.CEL GSM276742.CEL
> norm 0.35700 0.967000 0.823000 1.000000
> 206427_s_at 13.33764 13.607918 13.190551 12.387189
> 205338_s_at 13.65492 12.812950 12.237476 12.912605
> 209848_s_at 13.48525 13.435389 13.851347 12.540495
> 205694_at 7.70928 10.045331 13.391456 11.103841
> 201909_at 12.47093 11.937344 6.631023 7.160071
> 208894_at 12.20508 8.892181 6.478889 5.927860
> 216512_s_at 13.42313 12.151691 11.620552 12.341763
> 205337_at 12.67544 12.036528 11.641203 12.275845
> 201850_at 11.85481 13.172666 12.964316 12.156142
> 210982_s_at 11.49940 8.380404 6.121762 5.921634
> GSM276743.CEL GSM276744.CEL GSM276745.CEL GSM276747.CEL
> norm 0.899000 0.927000 0.754000 0.437000
> 206427_s_at 12.665097 12.604673 11.446630 13.000295
> 205338_s_at 13.261141 12.448096 13.185698 12.510952
> 209848_s_at 13.396711 13.882529 13.040600 12.984137
> 205694_at 10.888474 7.094063 8.630120 12.321685
> 201909_at 12.100560 6.666787 12.330600 6.572282
> 208894_at 7.741437 8.348155 10.106442 6.009902
> 216512_s_at 12.830373 11.504074 12.300163 11.525958
> 205337_at 12.264569 11.676281 11.940917 11.618351
> 201850_at 11.055564 12.202366 7.327056 12.853055
> 210982_s_at 7.285289 8.129298 9.577032 5.924993
> GSM276748.CEL GSM276752.CEL GSM276754.CEL GSM276756.CEL
> norm 0.321000 0.620000 0.155000 0.946000
> 206427_s_at 9.081283 11.446978 8.191261 13.192507
> 205338_s_at 13.737773 13.698520 12.983830 10.948681
> 209848_s_at 13.234025 12.956672 10.644642 13.176656
> 205694_at 7.953865 7.397013 7.170732 13.618932
> 201909_at 12.533684 7.049442 6.804030 7.135974
> 208894_at 11.868729 8.558455 6.629858 6.850639
> 216512_s_at 13.589290 12.781853 12.060414 10.143297
> 205337_at 13.084386 12.442617 12.104849 10.364035
> 201850_at 6.615453 8.104145 7.058739 6.514298
> 210982_s_at 11.058085 7.891520 6.516261 6.532226
> GSM276758.CEL GSM276759.CEL
> norm 0.767000 0.218000
> 206427_s_at 5.742074 11.232337
> 205338_s_at 6.375289 13.406557
> 209848_s_at 6.226996 6.835458
> 205694_at 5.864042 11.218719
> 201909_at 6.907489 7.316435
> 208894_at 12.596987 12.408412
> 216512_s_at 6.308256 12.318892
> 205337_at 6.063775 12.389912
> 201850_at 6.816491 6.602764
> 210982_s_at 11.985288 11.853911
>
> *What I did is the following:*
>>fm1=as.formula((norm) ~ "206427_s_at" + "205338_s_at" + "209848_s_at" +
> "205694_at" + "201909_at" + "208894_at" + "216512_s_at" + "205337_at" +
> "201850_at" + "210982_s_at")
>>lm1=lm(fm1,data1new)
>
> And I receive the following error:
> Error in terms.formula(formula, data = data) :
> invalid model formula in ExtractVars
>
>
> *I have also tried:*
>>cols=rownames(data3) %%%%Where data3 is the same data frame with data
> above, but without the "norm" row binded yet
> thus: > cols
> [1] "206427_s_at" "205338_s_at" "209848_s_at" "205694_at" "201909_at"
> [6] "208894_at" "216512_s_at" "205337_at" "201850_at" "210982_s_at"
>
>> lm1=lm(fm1,data1new)
>
> and in this case Ireceive the following error:
> Error in model.frame.default(formula = fm1, data = data1new,
> drop.unused.levels = TRUE) :
> variable lengths differ (found for 'cols')
>
> Could anyone help me with this?
>
> Thank you very much in advance,
> Eleni
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org
More information about the Bioconductor
mailing list