Question

Help with error using camera() in limma

0

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Chris ▴ 20

@3fdb6f97

Last seen 3 months ago

United States

Hi all,

After googling and ask chatGPT, I don't know how to fix this error. Would you please have a suggestion? Thank you so much!

gene_sets_dir <- "gene_sets"
c2_gmt_url <- "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2023.2.Hs/c2.all.v2023.2.Hs.entrez.gmt"
c2_gmt_file <- file.path(
  gene_sets_dir,
  "c2.all.v2023.2.Hs.entrez.gmt"
c2_list <- qusage::read.gmt(c2_gmt_file) # geneSets <- getGmt(c2_gmt_file) also get the same error. GeneSets is large genesetcollection.

w <- arrayWeights(numeric_matrix, design) 
fit <- lmFit(numeric_matrix, design, weights=w)
cameraRes <- camera(fit, c2_list, inter.gene.cor=0.01) # fit is large MArrayLM, c2_list is large list.

Error in getEAWP(y) : data object isn't of a recognized data class

I guess the c2_list or geneSets is not in the correct format.

CAMERA limma • 589 views

ADD COMMENT • link 7 months ago Chris ▴ 20

score 2 · Accepted Answer · 2024-04-30

2

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 10 hours ago

United States

The first step should be to read the help page, which says

Usage:

     ## Default S3 method:
     camera(y, index, design, contrast = ncol(design), weights = NULL,
            use.ranks = FALSE, allow.neg.cor=FALSE, inter.gene.cor=0.01, trend.var = FALSE,
            sort = TRUE, ...)
     ## Default S3 method:
     cameraPR(statistic, index, use.ranks = FALSE, inter.gene.cor=0.01, sort = TRUE, ...)
     interGeneCorrelation(y, design)

Arguments:

       y: a numeric matrix of log-expression values or log-ratios of
          expression values, or any data object containing such a
          matrix.  Rows correspond to probes and columns to samples.
          Any type of object that can be processed by 'getEAWP' is
          acceptable.  'NA' or infinite values are not allowed.

An MArrayLM object is none of the choices for the first argument.

ADD COMMENT • link 7 months ago James W. MacDonald 67k

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Thanks James! That is a great tip.

cameraRes <- camera(numeric_matrix, geneSets, inter.gene.cor=0.01, design)
Error in Stat[iset] : invalid subscript type 'S4'

Now I guess the error is because geneSets is not in the correct format but I don't know how to fix.

ADD REPLY • link 7 months ago Chris ▴ 20

1

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Again, this is where you need to read the help page and try to diagnose. It says

 index: an index vector or a list of index vectors.  Can be any
          vector such that 'y[index,]' of 'statistic[index]' selects
          the rows corresponding to the test set.  The list can be made
          using 'ids2indices'.

And if you do ?read.gmt it says the output is a list, with each item representing a gene set. Most likely the gene sets are just gene symbols. Unless the row.names of your 'y' object are the same thing as the values in your geneSets list, y[index] isn't going to select the rows corresponding to the gene set, right?

ADD REPLY • link 7 months ago James W. MacDonald 67k

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Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.

ADD REPLY • link 7 months ago Chris ▴ 20