Question

Problem concerning the Probe_Id / ProbeID and illuminaHumanv4PROBEQUALITY

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malte.hermes • 0

@maltehermes-20450

Last seen 5.5 years ago

hi, i've come across the following problem: the illuminaHumanv4PROBEQUALITY uses the "ProbeId" of the form e.g "ILMN3165565" whereas I was using the "ProbeID" which is just a number like "4230047" this is probably why I only get "no match"

when changing the ProbeID to Probe_Id in the readBeadSummaryData function:

BSData = readBeadSummaryData(dataFile = dataFile, sep="\t",ProbeID = "Probe_Id", skip = 0, columns = list(exprs = ".mean",se.exprs=".sd", nObservations = ".nbeads", Detection = "pvalue"))

I get the following Error:

Error in .rowNamesDF<-(x, value = value) : invalid 'row.names' length

Does anybody know what to do or got a similar problem? Thanks in advance Malte

sessioninfo()

R version 3.5.3 (2019-03-11) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LCCOLLATE=GermanGermany.1252 LCCTYPE=GermanGermany.1252
[3] LCMONETARY=GermanGermany.1252 LCNUMERIC=C
[5] LCTIME=German_Germany.1252

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods
[9] base

other attached packages: [1] illuminaHumanv4.db1.26.0 org.Hs.eg.db3.7.0 AnnotationDbi1.44.0
[4] IRanges2.16.0 S4Vectors0.20.1 limma3.36.5
[7] affy1.60.0 beadarray2.32.0 ggplot23.1.0.9000
[10] Biobase2.42.0 BiocGenerics_0.28.0

illuminaHumanv4PROBEQUALITY • 1.2k views

ADD COMMENT • link updated 5.5 years ago by James W. MacDonald 67k • written 5.5 years ago by malte.hermes • 0

score 0 · Answer 1 · 2019-04-09

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 22 minutes ago

United States

Your question is difficult to answer because you seem to be omitting critical information, like what you have done, what you got, what you are trying to do, etc.

That said, do note that R is case sensitive, and 'ProbeId' is not the same thing as 'PROBEID'. And if I am not mistaken, the column you are after is the latter, not the former.

ADD COMMENT • link 5.5 years ago James W. MacDonald 67k

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I'm sorry I didn't properly explain my problem. The main Problem is: in my txt. file there are two forms of ID one is the ILMN.... number which I'l need later to match my Probes to the ones in the "illuminaHumanv4PROBEQUALITY"

when using this ID in the function

readBeadSummaryData(dataFile = dataFile, sep="\t",ProbeID = "Probe_Id", skip = 0, columns = list(exprs = ".mean",se.exprs=".sd", nObservations = ".nbeads", Detection = "pvalue"))

I get the following Error:

Error in .rowNamesDF<-(x, value = value) : invalid 'row.names' length

and this must be somehow because of the ID as when I use the other (ProbeID which are unique numbers without ILMN) it works fine.

So either I need to find out why this error emerges and fix it, or I need to know how to add this Illumina ID (ILMN) later in order to subset and match the data.

I hope this did a better job in explaining the problem.

ADD REPLY • link 5.5 years ago malte.hermes • 0

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I don't use beadarray, personally, as any Illumina data I get can be read in using read.ilmn in limma. And a quick download of some Illumina Human HT12 v4 data from GEO indicates to me that there isn't a column called Probe_Id, so I'll have to take your word on that one. I also cannot find a function called .rowNamesDF, so you could run traceback right after the error to see where that function comes from and possibly debug yourself.

That said, what you have is a matching problem. You have a column of IDs that you want to use, and a column of IDs that you end up getting. It's a simple thing to map one to the other using match.

> d.f1 <- data.frame(badids = paste0("ILMN_", 1:15), data = rnorm(15))
> d.f2 <- data.frame(badids = paste0("ILMN_", sample(1:15, 15)), goodids = sample(1e6:5e6, 15))

> d.f1
    badids         data
1   ILMN_1  0.228933286
2   ILMN_2 -1.158914311
3   ILMN_3  1.895216716
4   ILMN_4 -0.006315407
5   ILMN_5 -0.918169608
6   ILMN_6  0.134903865
7   ILMN_7  0.303527312
8   ILMN_8 -0.437561000
9   ILMN_9  0.353635970
10 ILMN_10  0.130136773
11 ILMN_11 -0.325654051
12 ILMN_12  0.888898599
13 ILMN_13 -0.072501702
14 ILMN_14 -0.586316096
15 ILMN_15  0.497953429

> d.f2
    badids goodids
1   ILMN_8 3053861
2  ILMN_14 4901544
3   ILMN_2 1172448
4   ILMN_4 1297134
5  ILMN_13 2756307
6   ILMN_6 3760236
7   ILMN_7 2132605
8   ILMN_1 1789266
9  ILMN_12 2692584
10 ILMN_10 4133025
11  ILMN_3 2468387
12 ILMN_15 3548859
13  ILMN_5 2731722
14 ILMN_11 4722814
15  ILMN_9 2709564

> d.f1$goodids <- d.f2[match(d.f1$badids, d.f2$badids),2]
> d.f1
    badids         data goodids
1   ILMN_1  0.228933286 1789266
2   ILMN_2 -1.158914311 1172448
3   ILMN_3  1.895216716 2468387
4   ILMN_4 -0.006315407 1297134
5   ILMN_5 -0.918169608 2731722
6   ILMN_6  0.134903865 3760236
7   ILMN_7  0.303527312 2132605
8   ILMN_8 -0.437561000 3053861
9   ILMN_9  0.353635970 2709564
10 ILMN_10  0.130136773 4133025
11 ILMN_11 -0.325654051 4722814
12 ILMN_12  0.888898599 2692584
13 ILMN_13 -0.072501702 2756307
14 ILMN_14 -0.586316096 4901544
15 ILMN_15  0.497953429 3548859

ADD REPLY • link 5.5 years ago James W. MacDonald 67k