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xlucpu / MOVICS

Multi-Omics integration and VIsualization in Cancer Subtyping
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getClustNum() error #10

Closed wjaratlerdsiri closed 1 year ago

wjaratlerdsiri commented 2 years ago

Hi,

I ran a problem with my copy number data in a position by sample matrix. Binary data of mutations are ok.

Part of my copy number

[TAB] BRA08.T BRA10.T BRA13.T BRA15.T KAL0004.T 1_108276812_108276812 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127 1_108276813_108286811 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127 1_108286812_108286812 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127 1_108286813_108296810 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127 1_108296811_108296811 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127 1_108296812_108306810 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127 [TAB] KAL0013.T KAL0022.T KAL0043.T KAL0054.T KAL0072.T 1_108276812_108276812 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276 1_108276813_108286811 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276 1_108286812_108286812 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276 1_108286813_108296810 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276 1_108296811_108296811 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276 1_108296812_108306810 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276

Command

Hrpcaall <- list(omics1 = Hrpcassm_mat, omics2 = Hrpcacna_data )

optk.hrpca <- getClustNum(data = Hrpcaall, is.binary = c(T,F), try.N.clust = 2:6, fig.name = "CLUSTER NUMBER")

Error

90% complete 95% complete 100% complete calculating Gap-statistics... Error in svd(B, nv = 0) : infinite or missing values in 'x' Calls: getClustNum ... -> msvd -> svd.sol -> nsmall.svd -> svd Execution halted

I tried to transform data by adding +20 or round numbers to 3 digits. It still didn't work. I am not sure what causes the error. It seems not to be negative numbers. Or is it about column names? Your suggestion would be appreciated. I tried to debug myself for many days.

Thanks, James

xlucpu commented 2 years ago

Really sorry for the delayed response.

It seems that your data cannot meet the requirement for one of the interatige clustering algorithm. I would suggest that you follow the vigneete and run each algorithm one by one to see which algoirthm causes such error, and start by then to check the data.

Best!

Marchy-Lulu commented 1 month ago

80% complete 85% complete 85% complete 90% complete 90% complete 95% complete 95% complete 100% complete calculating Gap-statistics... Error in crossprod(x$t) :"crossprod" is not a BUILTIN function.

According to the experience post website before, I tried to transform data round numbers to 3 digits. It still didn't work. I am not sure what causes the error.

Thanks， Marchy