CCLE expression data file explaination (CCLE_Expression_2012-09-29.res)

Question

[Mike]

Hi all,

I have CCLE expression data file "CCLE_Expression_2012-09-29.res" downloaded from CCLE Broad broadinstitute.org). Could you please help me what are "A", "P" and "M" columns in data matrix file.

example data file (CCLE_Expression_2012-09-29.res)

Description     Accession       LN18_CENTRAL_NERVOUS_SYSTEM              769P_KIDNEY              786O_KIDNEY  ....n

PTPN21  1320_at                  5.063595                                                       P       4.377036             A       4.289519        A     .....n

Thanks in advance.

Answer 1

[tszn1984]

Detection: the call that indicates whether the transcript is detected (P present), undetected ( A, absent), or at the limit of detection (M, marginal). Ref: http://www.ohsu.edu/xd/research/research-cores/gene-profiling-shared-resource/project-design/array-technology/affymetrix-genechip-arrays.cfm

[Mike]

Thank you very much @tszn1984, so what do you mean by detection ? undetected mean not expressed? Am I right ? but in above example cell line (7860_KIDNEY, gene/probe= PTPN21/1320_at, expression value = 4.289519, and detection = A). how to proceed this data ? should I exclude all undetected samples ?

Thanks