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Question: How can I pre-process illumina raw file
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gravatar for Agaz Hussain Wani
3 months ago by
India
Agaz Hussain Wani240 wrote:

I have some raw `Illumina` data and when processing with `lumi` R package,  gives some error.

Actually I pre-process some other data which works fine by using the following code

x.lumi <- lumiR("filename")

lumiExpr <- lumiExpresso(x.lumi, bg.correct = TRUE, normalize = TRUE, verbose = TRUE)

exprs <- exprs(lumiExpr)

pvalue <- detection(lumiExpr)

But when I try to process the data  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52519, which looks something like

ID_REF    Sample 1.2.    Detection Pval    Sample 2.    Detection Pval    Sample 3.    Detection Pval    Sample 4.    Detection Pval    Sample 5.    Detection Pval    Sample 6.    Detection Pval    Sample 7.    Detection Pval    Sample 8.    Detection Pval    Sample 2.2.    Detection Pval    Sample 10.    Detection Pval    Sample 11.    Detection Pval    Sample 12.    Detection Pval
ILMN_1762337    43    0.28063    36.7    0.75758    41.5    0.55336    31.4    0.92754    35.2    0.88406    37.4    0.70619    34.4    0.80632    36.5    0.86561    39    0.89987    36.8    0.83399    44.1    0.36232    42.2    0.29381
ILMN_2055271    41.4    0.4361    51.1    0.01449    46.8    0.13175    35.7    0.5336    44.3    0.13307    43.7    0.13043    38.9    0.34519    44.1    0.16601    46.1    0.278    43.7    0.19499    43.4    0.4361    52    0.01976
ILMN_1736007    43.2    0.26746    41.2    0.29908    46.6    0.14098    38.6    0.23584    44.9    0.10408    38.1    0.639    37    0.54809    42.3    0.28459    52.2    0.04348    41.1    0.4282    46.3    0.20685    41.3    0.37813
ILMN_2383229    46    0.10804    51.6    0.01449    46    0.16996    36.3    0.4585    37.2    0.7365    39.2    0.5112    40.3    0.20553    43.3    0.20158    38.8    0.90777    36.6    0.85771    39.3    0.84058    37.9    0.72596
ILMN_1806310    43    0.28063    62.5    0.00527    47.9    0.09091    36.5    0.42951    43    0.20026    43.2    0.15547    36.2    0.63636    40.6    0.44664    48.6    0.12912    42.1    0.31752    47.7    0.12912    40.4    0.45982

I get the error

Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds

Why there is a problem and how can I process such data.

 

ADD COMMENTlink modified 3 months ago by James W. MacDonald45k • written 3 months ago by Agaz Hussain Wani240

What do you mean by 'process the data'? You gave code that worked, but not the code that didn't work! How are people to help if you don't show what you did, and what happened?

ADD REPLYlink written 3 months ago by James W. MacDonald45k

'process the data', I mean to generate expression values and p-values from the raw data. The same code is used for both the files.

ADD REPLYlink written 3 months ago by Agaz Hussain Wani240
0
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald45k wrote:

You are trying to process already processed data. If you want to re-run using lumi, you need to get the raw data, using e.g., getGEOSuppFiles from the GEOquery package.

ADD COMMENTlink written 3 months ago by James W. MacDonald45k
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