Question: mas5calls error question
0
gravatar for suarez.samuel
4.0 years ago by
United States
suarez.samuel0 wrote:

Hello All,

    I am attempting to use the mas5calls function to get present/absent calls on a large collection of microarray data that I am attempting to analyze. I will admit I am new to this type of analysis and am looking for some direction to correct the error I am receiving. My error is produced as follows:

> callsESet <- mas5calls(affy_liver_qc)
Getting probe level data...
Computing p-values
Error in `colnames<-`(`*tmp*`, value = c("95686.CEL", "95703.CEL", "95746.CEL", :
length of 'dimnames' [2] not equal to array extent

What does this error signify and how can I correct it? What is the package telling me I need to fix?

Thanks,

Sam

ADD COMMENTlink modified 4.0 years ago by James W. MacDonald51k • written 4.0 years ago by suarez.samuel0
Answer: mas5calls error question
0
gravatar for James W. MacDonald
4.0 years ago by
United States
James W. MacDonald51k wrote:

The most likely answer is that the files you are trying to analyze are PM-only arrays, in which case it isn't possible to compute conventional MAS5.0 calls. I believe the xps package will allow you to estimate something similar for PM-only arrays, and both xps and oligo offer dabg and psdabg calls (paCalls() in oligo), which are supposed to be equivalent measures for PM-only arrays.

ADD COMMENTlink written 4.0 years ago by James W. MacDonald51k

Thanks for your answer, James. My data all comes from the Affymetrix rat genome 230 2.0 array, and multiple papers have indicated that the arrays have been examined for present, marginal, or absent calls. Is the method I am using not suited to these PMA arrays?

ADD REPLYlink written 4.0 years ago by suarez.samuel0

No, those arrays are PM/MM arrays, so it should work. Is 'affy_liver_qc' an AffyBatch?

ADD REPLYlink written 4.0 years ago by James W. MacDonald51k

In environment - values in RStudio, 'affy_liver_qc' is annotated as a 'Large AffyBatch (1.2 Mb)

ADD REPLYlink written 4.0 years ago by suarez.samuel0

I can't reproduce your error:

> library(GEOquery)
> getGEOSuppFiles("GSE31668")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE31nnn/GSE31668/suppl/
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE31nnn/GSE31668/suppl//GSE31668_RAW.tar'
downloaded 17.1 MB

trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE31nnn/GSE31668/suppl//filelist.txt'
downloaded 452 bytes
> setwd("GSE31668/")
> untar("GSE31668_RAW.tar")
> library(affy)
> abatch <- ReadAffy()
> abatch

AffyBatch object
size of arrays=834x834 features (19 kb)
cdf=Rat230_2 (31099 affyids)
number of samples=6
number of genes=31099
annotation=rat2302
notes=

> mcalls <- mas5calls(abatch)
Getting probe level data...
Computing p-values
Making P/M/A Calls
> mcalls
ExpressionSet (storageMode: lockedEnvironment)
assayData: 31099 features, 6 samples
  element names: exprs, se.exprs
protocolData
  sampleNames: GSM786182_DAPT1.CEL.gz GSM786183_DAPT2.CEL.gz ...
    GSM786187_DMSO3.CEL.gz (6 total)
  varLabels: ScanDate
  varMetadata: labelDescription
phenoData
  sampleNames: GSM786182_DAPT1.CEL.gz GSM786183_DAPT2.CEL.gz ...
    GSM786187_DMSO3.CEL.gz (6 total)
  varLabels: sample
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: rat2302
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252 
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                        
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base     

other attached packages:
[1] rat2302cdf_2.18.0   affy_1.48.0         GEOquery_2.36.0  
[4] Biobase_2.30.0      BiocGenerics_0.16.1

loaded via a namespace (and not attached):
[1] IRanges_2.4.3         XML_3.98-1.3          bitops_1.0-6       
[4] DBI_0.3.1             stats4_3.2.2          RSQLite_1.0.0      
[7] BiocInstaller_1.20.1  zlibbioc_1.16.0       affyio_1.40.0      
[10] S4Vectors_0.8.3       preprocessCore_1.32.0 tools_3.2.2        
[13] RCurl_1.95-4.7        compiler_3.2.2        AnnotationDbi_1.32.0
>

Can you get what I just did to work?

ADD REPLYlink written 4.0 years ago by James W. MacDonald51k

I replicated your testing above and it appears to work.

> library(GEOquery)
Setting options('download.file.method.GEOquery'='curl')
> getGEOSuppFiles("GSE31668")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE31nnn/GSE31668/suppl/
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0 17.0M    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0  0 17.0M    0  9576    0     0  22679      0  0:13:09 --:--:--  0:13:09  116k 46 17.0M   46 8080k    0     0  5765k      0  0:00:03  0:00:01  0:00:02 7630k 93 17.0M   93 15.9M    0     0  6788k      0  0:00:02  0:00:02 --:--:-- 7914k100 17.0M  100 17.0M    0     0  6886k      0  0:00:02  0:00:02 --:--:-- 7957k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0   452    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0113   452  113   452    0     0   1155      0 --:--:-- --:--:-- --:--:--  9416
> setwd("~/GSE31668")
> untar("GSE31668_RAW.tar")
> library(affy)

>abatch
AffyBatch object
size of arrays=834x834 features (19 kb)
cdf=Rat230_2 (31099 affyids)
number of samples=6
number of genes=31099
annotation=rat2302
notes=

abatch <- ReadAffy()
> mcalls <- mas5calls(abatch)
Getting probe level data...
Computing p-values
Making P/M/A Calls
> mcalls
ExpressionSet (storageMode: lockedEnvironment)
assayData: 31099 features, 6 samples
  element names: exprs, se.exprs
protocolData
  sampleNames: GSM786182_DAPT1.CEL.gz GSM786183_DAPT2.CEL.gz ...
    GSM786187_DMSO3.CEL.gz (6 total)
  varLabels: ScanDate
  varMetadata: labelDescription
phenoData
  sampleNames: GSM786182_DAPT1.CEL.gz GSM786183_DAPT2.CEL.gz ...
    GSM786187_DMSO3.CEL.gz (6 total)
  varLabels: sample
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: rat2302
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rat2302cdf_2.16.0    GEOquery_2.34.0      BiocInstaller_1.18.5 affy_1.46.1         
[5] Biobase_2.28.0       BiocGenerics_0.14.0

loaded via a namespace (and not attached):
 [1] IRanges_2.2.9         XML_3.98-1.3          bitops_1.0-6          GenomeInfoDb_1.4.3   
 [5] DBI_0.3.1             stats4_3.2.2          RSQLite_1.0.0         zlibbioc_1.14.0      
 [9] affyio_1.36.0         S4Vectors_0.6.6       preprocessCore_1.30.0 tools_3.2.2          
[13] RCurl_1.95-4.7        AnnotationDbi_1.30.1

I'm able to reproduce what you accomplished above.

 

 
ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by suarez.samuel0

in my separate project for testing, I have imported my affy_liver_qc affybatch value. I was able to run

mas5calls(affy_liver_qc)

and received no errors. I switched to my working directory project, ran:

> callsESet<-mas5calls(affy_liver_qc)
Getting probe level data...
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’

Computing p-values
Error in `colnames<-`(`*tmp*`, value = c("95686.CEL", "95703.CEL", "95746.CEL",  :
  length of 'dimnames' [2] not equal to array extent

I am unsure as to how to proceed.

 
ADD REPLYlink written 4.0 years ago by suarez.samuel0

You probably have a .Rdata file in your working directory that has something in it that is messing things up, so maybe you should try starting R using --vanilla so you don't load that in. In addition, it seems like you have the wrong versions of Bioconductor packages for that version of R. You should upgrade, following the instructions here.

ADD REPLYlink written 4.0 years ago by James W. MacDonald51k
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