dhimmel
commented
1 year ago Hey @afaissa, this isn't an official repo for LINCS, just a project that processed LINCS data. So this is probably not the right location for your question. Nonetheless, feel free to comment below if you find an answer elsewhere, since perhaps people will stumble upon this issue with the same question.
I am trying to plot some genes using data level 4 for my compound (BRD-K55591206) on HepG2 cells.
There are two signatures with HepG2 cells at level 5: LJP008_HEPG2_24H:J01 POL001_HEPG2_24H:J09 To make sure I was using the same data from these level 5 signatures I checked the replicates at level 4 of each of these signatures above. The average of the two LJP008 experiments (distil_ids: LJP008_HEPG2_24H_X2_B20:J01|LJP008_HEPG2_24H_X3_B20:J01) matches the signature of each gene at level 5. Perfect.
However, the level 4 data for signature POL001_HEPG2 (distil_ids: POL001_HEPG2_24H_X1.L2_B23:J07|POL001_HEPG2_24H_X2.L2_B23:J07|POL001_HEPG2_24H_X3.L2_B23:J07) does not match level 5.
If we use the NAT2 gene as an example, we have the following level 5 value: 0.004413
On the other hand, the values for the level 4 replicates are: POL001_HEPG2_24H_X1.L2_B23:J07 = -0.386299998 POL001_HEPG2_24H_X2.L2_B23:J07 = 0.110600002 POL001_HEPG2_24H_X3.L2_B23:J07 =0.38409999 The avg 0.036133 does not match level 5 0.004413
The compound is BRD-K55591206, 10 µM, 24 h.
Why don’t they match?
I am using cmapR to retrieve the data from these files: https://clue.io/releases/data-dashboard https://s3.amazonaws.com/macchiato.clue.io/builds/LINCS2020/level5/level5_beta_trt_cp_n720216x12328.gctx https://s3.amazonaws.com/macchiato.clue.io/builds/LINCS2020/level4/level4_beta_all_n3026460x12328.gctx https://s3.amazonaws.com/macchiato.clue.io/builds/LINCS2020/siginfo_beta.txt https://s3.amazonaws.com/macchiato.clue.io/builds/LINCS2020/instinfo_beta.txt