Formula for linear regression and r-squared

General
1

Good Afternoon. Which formula should I use for R-squared?

The data set is listed below. I tried using the formula:
lm(formula = y ~ A2M + A4GNT + AAAS + AACS + AADAC)

However, I keep getting: "Error in eval(predvars, data, env)"

source(system.file("extdata", "patientselection.config", package = "curatedOvarianData"))
set.seed(123)
data("TCGA_eset")
varLabels(TCGA_eset)
[1] "alt_sample_name"
[2] "unique_patient_ID"
[3] "sample_type"
[4] "histological_type"
[5] "primarysite"
[6] "arrayedsite"
[7] "summarygrade"
[8] "summarystage"
[9] "tumorstage"
[10] "substage"
[11] "grade"
[12] "age_at_initial_pathologic_diagnosis"
[13] "pltx"
[14] "tax"
[15] "neo"
[16] "days_to_tumor_recurrence"
[17] "recurrence_status"
[18] "days_to_death"
[19] "vital_status"
[20] "os_binary"
[21] "relapse_binary"
[22] "site_of_tumor_first_recurrence"
[23] "primary_therapy_outcome_success"
[24] "debulking"
[25] "percent_normal_cells"
[26] "percent_stromal_cells"
[27] "percent_tumor_cells"
[28] "batch"
[29] "flag"
[30] "flag_notes"
[31] "uncurated_author_metadata"
mat.gene = exprs(TCGA_eset)
y = mat.gene[1,]
x = t(mat.gene[2:6,])
dd = cbind(y, x)
dd = as.data.frame(na.omit(dd))
head(dd)
y A2M A4GNT AAAS AACS AADAC
TCGA.20.0987 2.923522 10.353008 3.321405 4.608010 7.279213 4.605331
TCGA.23.1031 3.052169 11.635772 3.666463 5.142133 7.048869 5.775611
TCGA.24.0979 2.846371 7.954542 3.258038 5.025422 7.750161 3.846412
TCGA.23.1117 3.002209 9.971500 3.596212 5.139928 6.206031 4.468379
TCGA.23.1021 3.062993 8.971334 3.388706 5.256831 7.835422 4.415817
TCGA.04.1337 2.974734 9.042876 3.269979 4.667723 6.763047 4.159804
tail(dd)
y A2M A4GNT AAAS AACS AADAC
TCGA.24.1852 2.804569 7.952748 3.266449 5.032060 7.181784 3.780469
TCGA.29.1692 2.993727 9.068691 3.542584 4.877798 7.580572 8.451190
TCGA.13.1817 3.136917 10.198890 3.336109 4.709619 5.921329 4.546632
TCGA.61.1916 2.965996 9.699037 3.405650 5.145519 8.360284 6.119431
TCGA.29.1704 3.157896 8.336289 3.323166 4.957783 5.700931 4.066970
TCGA.13.1819 2.934607 8.661028 3.307428 5.404119 6.553031 4.178920

2

Hi,

I noticed in the lm() call you posted that you are missing a the data = argument. You're formula references columns that might not be in memory because they are columns in your data frame and not individual variables. Is dd the data frame with the columns you want in your model?

So instead of:

You might consider:

lm(formula = y ~ A2M + A4GNT + AAAS + AACS + AADAC, data = dd)

I hope that helps!

3

Thanks! I got it. It now works!

4

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