I have analyzed the dataset of GSE38132 from gene expression omnibus. The is from cell line breast cancer ZR-75-1 which comprises of 9 conditions with 4 replicates for each condition making it 36 samples. I used limma package to normalize the data (quantile normalization). I noticed a great change in a group where three replicates shows similar expression where the 4th replicate of the same sample is different from all other three. I confirmed the expression from raw data by cross checking with the probe id and found 1 replicate is different from all other three. As a double validation I checked the normalized sample deposited in NCBI-GEO and I found the same. Is this possible? Please see the heat map first four are replicates from the same sample
