Question

mas5calls function doesn't work; mirna40cdf problem

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Berna • 0

@bc6afe81

Last seen 21 months ago

Germany

setwd("microArray/A549_ALI(1)/A549_ALI/4_tert-Butanol (22)/")
list.celfiles()
my.affy=ReadAffy()
my.calls <- mas5calls(my.affy)

This is my code and and up to my.affy it works. Then I get this error message:

my.calls <- mas5calls(my.affy)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Error in getCdfInfo(object) : 
    Could not obtain CDF environment, problems encountered:
 Specified environment does not contain miRNA-4_0
 Library - package mirna40cdf not installed
 Bioconductor - mirna40cdf not available

The answers I got here in the forum have unfortunately brought me nothing. I would like to use the mas5calls function.

Thanks for all answers.

R Bioconductor mas5calls • 1.6k views

ADD COMMENT • link updated 22 months ago by James W. MacDonald 67k • written 22 months ago by Berna • 0

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Please see related post: miRNA microarray analysis

ADD REPLY • link 22 months ago shepherl 4.1k

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As mentioned before, this answer did not help me.

ADD REPLY • link 22 months ago Berna • 0

score 1 · Answer 1 · 2023-02-03

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 21 minutes ago

United States

You cannot use mas5calls on a miRNA-4_0 array. There are no MM probes on that array, so it is not possible to get MAS-5.0 calls, because that requires a comparison between PM and MM probes.

ADD COMMENT • link 22 months ago James W. MacDonald 67k

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Thank you for the information. I did not know that. Would you have a tip how I could proceed differently?

ADD REPLY • link 22 months ago Berna • 0

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Yes. Follow the recommendation in the link that was provided to you by Lori Shepherd.

ADD REPLY • link 22 months ago James W. MacDonald 67k

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Also: you could consider using DABG for present/absent calls. James elaborated on this in this thread: Oligo package: paCalls questions

... and combine that with his insights in this thread: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0

ADD REPLY • link 22 months ago Guido Hooiveld ★ 4.1k

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Except that the miRNA arrays are sort of dumb. An miRNA is 21-23 nt long, and Affy probes are ... 25 nt long. So a 'probeset' for an Affy miRNA array is a bunch of identical 25-mers. Plus, they tend to be super dim, so it's hard to discern which probesets are being expressed and which aren't.

ADD REPLY • link 22 months ago James W. MacDonald 67k

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Thanks for all answers. I have tried, but still get an error message. Do you know how I can work around this?

    > library(pd.mirna.4.0)
    > library(oligo)
    > setwd("microArray/A549_ALI(1)/A549_ALI/4_tert-Butanol (22)/")
    > cel_Files <- oligoClasses::list.celfiles()
    > affyRaw <- oligo::read.celfiles(cel_Files)
    Lade nötiges Paket: pd.mirna.4.0
    Lade nötiges Paket: RSQLite
    Lade nötiges Paket: DBI
    Platform design info loaded.
    Reading in : (46) 22-B1-1_(miRNA-4_0).CEL
    Reading in : (47) 22-B1-2_(miRNA-4_0).CEL
    Reading in : (48) 22-B1-3_(miRNA-4_0).CEL
    Reading in : (49) 22-R1-1_(miRNA-4_0).CEL
    Reading in : (50) 22-NEC 1-1_(miRNA-4_0).CEL
    Reading in : (51) 22-B2-1_(miRNA-4_0).CEL
    Reading in : (52) 22-B2-2_(miRNA-4_0).CEL
    Reading in : (53) 22-B2-3_(miRNA-4_0).CEL
    Reading in : (54) 22-R2-1_(miRNA-4_0).CEL
    Reading in : (55) 22-NEC 2-1_(miRNA-4_0).CEL
    Reading in : (56) 22-B3-1_(miRNA-4_0).CEL
    Reading in : (57) 22-B3-2_(miRNA-4_0).CEL
    Reading in : (58) 22-B3-3_(miRNA-4_0).CEL
    Reading in : (59) 22-R3-1_(miRNA-4_0).CEL
    Reading in : (60) 22-NEC 3-1_(miRNA-4_0).CEL
    > paCalls_ <- paCalls(affyRaw, "PSDABG")
    Error in match.arg(method, "MAS5") : 'arg' should be “MAS5”
   > paCalls_ <- paCalls(affyRaw, "DABG")
   Error in match.arg(method, "MAS5") : 'arg' should be “MAS5”
   > paCalls_ <- paCalls(affyRaw, "MAS5")
   Getting probe level data... Error: no such table: mmfeature 
   > paCalls_2 <- oligo::paCalls(object = affyRaw)
   Getting probe level data... Error: no such table: mmfeature
   > paCalls_2 <- oligo::paCalls(object = affyRaw, "DABG")
   Error in match.arg(method, "MAS5") : 'arg' should be “MAS5”
   > paCalls_2 <- oligo::paCalls(object = affyRaw, "MAS5")
   Getting probe level data... Error: no such table: mmfeature

ADD REPLY • link 22 months ago Berna • 0

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The paCalls function in oligo is meant to do the MAS5.0 calls that you could have previously done using mas5calls with the affy package. As I mentioned already, you cannot compute MAS5.0 calls using an array that has no MM probes.

You will also face difficulties trying to filter out probesets on this array. These arrays are very dim, and it is difficult to distinguish between probesets that are measuring anything and those that are not. And there are not even enough on the array that filtering them out will gain you anything, so you would do better to quit trying to filter and just go forward with all the probesets.

ADD REPLY • link 22 months ago James W. MacDonald 67k