search

cran / MetaIntegrator

:exclamation: This is a read-only mirror of the CRAN R package repository. MetaIntegrator — Meta-Analysis of Gene Expression Data. Homepage: http://biorxiv.org/content/early/2016/08/25/071514
6 stars 1 forks source link

problem in processing the data for Metaintegrator #1

Open SaraMorsy opened 4 years ago

SaraMorsy commented 4 years ago

I have two problems with the package First I used getGEOData for importing and preprocessing the data, however, when I do the meta-analysis, I get this error

Error in runMetaAnalysis(exampleMetaObj, maxCores = 1) : In GSE5388 there are not @ least two cases and/or two controlsIn GSE46449 there are not @ least two cases and/or two controls

Here is the full code > yi<-getGEOData(gseVector = "GSE5388",formattedNames = "GSE5388",qNorm = T)

Found 1 file(s) GSE5388_series_matrix.txt.gz Using locally cached version: C:\Users\Sara\AppData\Local\Temp\RtmpcZNw3R/GSE5388_series_matrix.txt.gz Parsed with column specification: cols( .default = col_double(), ID_REF = col_character() ) See spec(...) for full column specifications. Using locally cached version of GPL96 found here: C:\Users\Sara\AppData\Local\Temp\RtmpcZNw3R/GPL96.soft Warning: 68 parsing failures. row col expected actual file 22216 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data 22217 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data 22218 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data 22219 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data 22220 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data ..... ....... .................. ......... ............ See problems(...) for more details.

`> gse5388<-yi$originalData$GSE5388

gse5388<-cleanUpPheno(gse5388) y<-getGEOData(gseVector = "GSE46449",formattedNames = "GSE46449",qNorm = T)` Found 1 file(s) GSE46449_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46449/matrix/GSE46449_series_matrix.txt.gz' Content type 'application/x-gzip' length 26331426 bytes (25.1 MB) downloaded 25.1 MB

Parsed with column specification: cols( .default = col_double(), ID_REF = col_character() ) See spec(...) for full column specifications. Using locally cached version of GPL570 found here: C:\Users\Sara\AppData\Local\Temp\RtmpcZNw3R/GPL570.soft Warning: 62 parsing failures. row col expected actual file 54614 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data 54615 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data 54616 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data 54617 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data 54618 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data ..... ....... .................. ......... ............ See problems(...) for more details.

> gse46449<-y$originalData$GSE46449 > gse46449<-cleanUpPheno(gse46449) > discovery_datasets <- list(gse46449, gse5388) > names(discovery_datasets) = c(gse5388$formattedName, gse46449$formattedName) > exampleMetaObj=list() > exampleMetaObj$originalData <- discovery_datasets > runMetaAnalysis(exampleMetaObj) Error in runMetaAnalysis(exampleMetaObj) : In GSE5388 there are not @ least two cases and/or two controlsIn GSE46449 there are not @ least two cases and/or two controls

SECOND Problem I have another problem regarding the preparation of data manually. I created csv file for each element of class, key, pheno and expr then converted them to matrix. However, when I check the format it gives me this error message (I have attached the files). How to convert it to matrix correctly?

> View(expr) > expr<-as.matrix(expr) > pheno<-as.matrix(pheno) >formattedName = "bipo1" >keys<-as.matrix(keys) >class<-as.vector(class) > datasetObject<list(class=class,expr=expr,keys=keys,pheno=pheno,formattedName=formattedName)

checkDataObject(datasetObject,"Dataset") Warning messages: 1: In .datasetCheckNull(dataset) : datasetObject$formattedName is null. The formatted name is missing 2: In .datasetCheckRowColNames(dataset) : The probes listed in expr and the probes listed in keys do not match. 3: In .datasetCheckRowColNames(dataset) : Class vector is not named. 4: In .checkClass(dataset) : Class vector is not a numeric vector. 5: In .datasetCheckType(dataset) : pheno must be a data frame. 6: In .datasetCheckType(dataset) : expr must be a numeric matrix. 7: In .datasetCheckType(dataset) : class must be either: 1) a numeric vector of 1's and 0's OR 2) NULL 8: In .datasetCheckType(dataset) : keys must be a vector.

What should I do?

gaborcsardi commented 4 years ago

Hi, this is a read only mirror of CRAN, please see the package authors in the DESCRIPTION file. Thanks!