Question

I have a tab-delimited file with several columns. I want only those rows whose pvalue < .05.

Probe    A_sig  A_Pval   B_sig  B_Pval   C_sig   C_Pval    D_sig   D_Pval
ILMN_122 12.31   0.04    23.6    0.4     124.5    0.04     567.4    0.008
ILMN_456 56.12   0       23.89   0.55    567.2    0.214    56.35    0.01 
ILMN_198 981.2   0.06    31.56   0.02    12.56    0.4      789.4    0.045
ILMN_980 876.0   0.001   124.7   0.01    167.3    0.12     245.7    0.35
ILMN_542 123.9   0.16    219.8   0.04    567.3    0.03     987.6    0.34 
ILMN_567 134.1   0       542.5   0.24    12.56    0.65     5.67     0.56 
ILMN_452 213.4   0.98    12.6    0.12    17.89    0.03     467.8    0.003 
ILMN_142 543.8   0.04    245.6   0.89    456.34   0.001    12.67    0.002 
ILMN_765 187.4   0.05    34.6    0.001   67.8     0.06     78.34    0.02

I need an output as follows:

     Probe  A_sig   A_Pval  B_sig     B_Pval   C_sig  C_Pval
   ILMN_122 12.31   0.04    32.56     0.004    311.4  0.001
   ILMN_980 876.0   0.001   123.4     0.001    678.9  0.02
   ILMN_142 543.8   0.04    56.56     0.015    67.8   0.04

Answer 1

Assuming that your data is in a data frame called mydata, you can select the rows you want by writing

  mydata[mydata$A_Pval<0.05 & mydata$B_Pval<0.05 & mydata$C_Pval<0.05,]

It might be easier to understand by doing it in multiple steps:

# gives a logical vector telling you if A_Pval is smaller than 0.05
significant_A <- mydata$A_Pval<0.05 

# gives a logical vector telling you if B_Pval is smaller than 0.05
significant_B <- mydata$B_Pval<0.05 

# gives a logical vector telling you if C_Pval is smaller than 0.05
significant_C <- mydata$C_Pval<0.05 

# combine the results to one logical vector
# significant_all[i] has value TRUE if all the p-values in row i 
# are smaller than 0.05

significant_all <- significant_A & significant_B & significant_C

# pick the rows you want
mydata[significant_all,]