Comments (1)
wgmao
commented on August 13, 2024
- The input to PLIER should be a gene-by-sample matrix where rows correspond to genes. It is unlikely given the message
Selecting common genes: 12549but it is good to double check. - The default option of PLIER() is to normalize the input as the first step where it z-scores every gene (row) using scale() function. If there are any genes with 0 standard deviation, you will get a lot of NA values and this will be a problem for rsvd(). If there are any NA values included in the input before scaling, this will lead to the same problem.
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Related Issues (16)
- Q-value error HOT 3
- rseed argument gives "error in Z %*% B : non-conformable arguments" HOT 2
- Adding Release Tag HOT 6
- Issue while running Tutorial HOT 8
- Prior data HOT 6
- Recommendation on the size of prior data? HOT 3
- Several questions about PLIER HOT 4
- Does these errors occur due to the small size of my dataset? HOT 2
- making a new pathways matrix HOT 14
- description of the outputs of PLIER() function HOT 4
- Problem with installing Rd object HOT 1
- Two question regarding interpretation of the pathways having significant AUC for a specific LV HOT 1
- Should the input gene expression data be log scale or not? HOT 2
- Can the data of mRNA of human tissue be use this method? HOT 8
- PLIER::num.pc error HOT 4
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