Hi Chris,

Please keep your posts on the list so you can get help from other people as well.

There are more than one column in your data that have their column names containing the keyword 'Probe', however the read.ilmn function expect there is only one such column so that it can properly assign probe identifiers to the probes. It looks the first column of your data contains the probe identifiers, so you should set 'probe=PROBE_ID' when you run read.ilmn.


Best wishes,

Wei


On Aug 17, 2013, at 4:33 AM, Chris Risothal wrote:

> Wei,
> 
> I am using the following command:
> 
> x <- read.ilmn(files="probe profile.txt", ctrlfiles="control probe profiles.txt")
> 
> My "probe profile.txt" does not contain header information, but here is the first line with two lines of data.
> 
> PROBE_ID	SYMBOL	9273370068_A.AVG_Signal	9273370068_A.Detection Pval	9273370068_A.NARRAYS	9273370068_A.ARRAY_STDEV	9273370068_A.BEAD_STDERR	9273370068_A.Avg_NBEADS	9273370068_B.AVG_Signal	9273370068_B.Detection Pval	9273370068_B.NARRAYS	9273370068_B.ARRAY_STDEV	9273370068_B.BEAD_STDERR	9273370068_B.Avg_NBEADS	9273370068_C.AVG_Signal	9273370068_C.Detection Pval	9273370068_C.NARRAYS	9273370068_C.ARRAY_STDEV	9273370068_C.BEAD_STDERR	9273370068_C.Avg_NBEADS	9273370068_D.AVG_Signal	9273370068_D.Detection Pval	9273370068_D.NARRAYS	9273370068_D.ARRAY_STDEV	9273370068_D.BEAD_STDERR	9273370068_D.Avg_NBEADS	9273370068_E.AVG_Signal	9273370068_E.Detection Pval	9273370068_E.NARRAYS	9273370068_E.ARRAY_STDEV	9273370068_E.BEAD_STDERR	9273370068_E.Avg_NBEADS	9273370068_F.AVG_Signal	9273370068_F.Detection Pval	9273370068_F.NARRAYS	9273370068_F.ARRAY_STDEV	9273370068_F.BEAD_STDERR	9273370068_F.Avg_NBEADS	9273370068_G.AVG_Signal	9273370068_G.Detection Pval	9273370068_G.NARRAYS	9273370068_G.ARRAY_STDEV	9273370068_G.BEAD_STDERR	9273370068_G.Avg_NBEADS	9273370068_H.AVG_Signal	9273370068_H.Detection Pval	9273370068_H.NARRAYS	9273370068_H.ARRAY_STDEV	9273370068_H.BEAD_STDERR	9273370068_H.Avg_NBEADS	9273370068_I.AVG_Signal	9273370068_I.Detection Pval	9273370068_I.NARRAYS	9273370068_I.ARRAY_STDEV	9273370068_I.BEAD_STDERR	9273370068_I.Avg_NBEADS	9273370068_J.AVG_Signal	9273370068_J.Detection Pval	9273370068_J.NARRAYS	9273370068_J.ARRAY_STDEV	9273370068_J.BEAD_STDERR	9273370068_J.Avg_NBEADS	9273370068_K.AVG_Signal	9273370068_K.Detection Pval	9273370068_K.NARRAYS	9273370068_K.ARRAY_STDEV	9273370068_K.BEAD_STDERR	9273370068_K.Avg_NBEADS	9273370068_L.AVG_Signal	9273370068_L.Detection Pval	9273370068_L.NARRAYS	9273370068_L.ARRAY_STDEV	9273370068_L.BEAD_STDERR	9273370068_L.Avg_NBEADS	SEARCH_KEY	ILMN_GENE	CHROMOSOME	DEFINITION	SYNONYMS	TargetID	ProbeID	SPECIES	SOURCE	TRANSCRIPT	SOURCE_REFERENCE_ID	REFSEQ_ID	UNIGENE_ID	ENTREZ_GENE_ID	GI	ACCESSION	PROTEIN_PRODUCT	ARRAY_ADDRESS_ID	PROBE_TYPE	PROBE_START	PROBE_SEQUENCE	PROBE_CHR_ORIENTATION	PROBE_COORDINATES	CYTOBAND	ONTOLOGY_COMPONENT	ONTOLOGY_PROCESS	ONTOLOGY_FUNCTION
> ILMN_1762337	7A5	236.0978	0.7441558	1	NaN	14.72377	22	262.2536	0.4545455	1	NaN	17.13116	21	259.018	0.4857143	1	NaN	20.26811	21	244.6225	0.5766234	1	NaN	13.17049	20	293.7429	0.1545455	1	NaN	19.53695	20	252.7831	0.4649351	1	NaN	14.87979	26	247.0036	0.4272727	1	NaN	9.686612	25	254.1092	0.5168831	1	NaN	25.24741	19	238.7411	0.5805195	1	NaN	11.25148	23	248.3546	0.4714286	1	NaN	14.3304	24	257.9403	0.5389611	1	NaN	18.90778	10	255.1144	0.4883117	1	NaN	15.00543	22	NM_182762.2	7A5	7	Homo sapiens putative binding protein 7a5 (7A5), mRNA.		7A5	6450255	Homo sapiens	RefSeq	ILMN_183371	NM_182762.2	NM_182762.2		346389	47271497	NM_182762.2	NP_877439.2	0006450255	S	2725	GTGTTACAAGACCTTCAGTCAGCTTTGGACAGAATGAAAAACCCTGTGAC	-	20147187-20147236	7p15.3e			
> ILMN_2055271	A1BG	317.0753	0.08961039	1	NaN	17.60022	12	365.0513	0.01948052	1	NaN	29.1449	17	362.9214	0.01688312	1	NaN	20.55249	22	297.9507	0.138961	1	NaN	23.81178	14	383.1979	0.007792208	1	NaN	24.62921	21	286.5022	0.1805195	1	NaN	14.57291	20	349.5719	0.02337662	1	NaN	29.1553	19	373.5414	0.01428571	1	NaN	22.20049	19	269.0879	0.2688312	1	NaN	13.6713	11	370.8822	0.01298701	1	NaN	29.8101	21	392.3283	0.01428571	1	NaN	41.74369	15	369.3197	0.01948052	1	NaN	20.21619	27	NM_130786.2	A1BG	19	Homo sapiens alpha-1-B glycoprotein (A1BG), mRNA.	A1B; GAB; HYST2477; ABG; DKFZp686F0970	A1BG	2570615	Homo sapiens	RefSeq	ILMN_175569	NM_130786.2	NM_130786.2		1	21071029	NM_130786.2	NP_570602.2	0002570615	S	3151	GGGATTACAGGGGTGAGCCACCACGCCCAGCCCCAGCTTAGTTTTTTAAA	-	63548541-63548590	19q13.43c	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite [goid 5576] [pmid 3458201] [evidence IDA]	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end [goid 8150] [evidence ND ]	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions [goid 3674] [evidence ND ]
> ILMN_1736007	A1BG	304.7664	0.1454545	1	NaN	22.61858	25	343.8062	0.03766234	1	NaN	24.54836	22	306.6519	0.1324675	1	NaN	18.23108	15	286.0155	0.1987013	1	NaN	18.77761	24	316.0644	0.06883117	1	NaN	22.10342	17	364.5466	0.02337662	1	NaN	23.77021	16	328.7427	0.03246753	1	NaN	22.41896	19	334.654	0.05194805	1	NaN	16.66162	23	295.7652	0.1246753	1	NaN	15.93948	30	324.818	0.04285714	1	NaN	15.19761	27	425.6782	0.005194805	1	NaN	42.57351	21	336.354	0.04415584	1	NaN	11.02559	15	NM_130786.2	A1BG	19	Homo sapiens alpha-1-B glycoprotein (A1BG), mRNA.	A1B; GAB; HYST2477; ABG; DKFZp686F0970	A1BG	6370619	Homo sapiens	RefSeq	ILMN_18893	NM_130786.2	NM_130786.2		1	21071029	NM_130786.2	NP_570602.2	0006370619	S	2512	GCAGAGCTGGACGCTGTGGAAATGGCTGGATTCCTCTGTGTTCTTTCCCA	-	63549180-63549229	19q13.43c	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite [goid 5576] [pmid 3458201] [evidence IDA]	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end [goid 8150] [evidence ND ]	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions [goid 3674] [evidence ND ]
> 
> 
> On Wed, Aug 14, 2013 at 1:46 AM, Wei Shi <shi@wehi.edu.au> wrote:
> Dear Josh,
> 
> Could you please provide the command you used and also the first 10 lines of your probe profile file? The read.ilmn function allows any number of columns to be included in your data files. It just extracts those columns whose names match the names specified in the parameters. So I do not know what caused your problem unless I can have a look at your data.
> 
> 
> Best regards,
> 
> Wei
> 
> 
> On Aug 14, 2013, at 12:30 PM, Josh [guest] wrote:
> 
> >
> > I have data exported from GenomeStudio (1.6) that I can correctly read and pre-process with lumi. However, when I try using read.ilmn in limma, I found that I get an error saying "Error in `rownames<-`(`*tmp*`, value = list(PROBE_ID = c("ILMN_1762337",  : length of 'dimnames' [1] not equal to array extent." I have found that this was due to the inclusion of extra columns in my probe profiles (TargetID, ProbeID, SPECIES, SOURCE, TRANSCRIPT and on). When I removed them, I can correctly read the probe and control profiles with read.ilmn. Is there a better fix around this than manually removing the columns?
> >
> > -- output of sessionInfo():
> >
> > R version 3.0.0 (2013-04-03)
> > Platform: x86_64-apple-darwin10.8.0 (64-bit)
> >
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> > attached base packages:
> > [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] lumi_2.12.0        Biobase_2.20.0     BiocGenerics_0.6.0 limma_3.16.2
> >
> > --
> > Sent via the guest posting facility at bioconductor.org.
> >
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