[BioC] problem reading GenePix files with .XLS extension

[Srinivas Iyyer]

this is Garber lung data.  there are 73 files.  they
all have this.xls extension and have the following
content.

!Exptid=5715
!Experiment Name=58-95_SCC
!Organism=Homo sapiens
!Category=Primary tumor
!Subcategory=Lung Cancer
!Description=mRNA from I. Petersen. Total RNA isloted
with Trizol. mRNA isolated with Invitrogen isolation
kit. Hyb by M. Garber.
!Experimenter=Mitchell Garber
!Contact email=garber at genome.stanford.edu
!Contact Address1=Genetics
!Contact Address2=L-311
!SlideName=shac046
!Printname=SHAC2
!Tip Configuration=Standard 32-tip
!Columns per Sector=28
!Rows per Sector=27
!Column Spacing=175
!Row Spacing=175
!Channel 1 Description=CRE reference
!Channel 2 Description=58-95_SCC
!Scanning Software=GenePix
!Software version=2.0.1.19
!Scanning parameters=
SPOT	NAME	Clone ID	Gene Symbol	Gene Name	Cluster ID
Accession	Preferred name	CH1D_MEDIAN	CH1I_MEDIAN
CH1_PER_SAT	CH1I_SD	CH1B_MEAN	CH1B_MEDIAN	CH1B_SD
CH1D_MEAN	CH2I_MEAN	CH2D_MEAN	CH2D_MEDIAN	CH2I_MEDIAN
CH2_PER_SAT	CH2I_SD	CH2B_MEAN	CH2B_MEDIAN	CH2B_SD
CH2BN_MEDIAN	CH2DN_MEAN	CH2IN_MEAN	CH2DN_MEDIAN
CH2IN_MEDIAN	CORR	DIAMETER	FLAG	LOG_RAT2N_MEAN
LOG_RAT2N_MEDIAN	PIX_RAT2_MEAN	PIX_RAT2_MEDIAN
PERGTBCH1I_1SD	PERGTBCH1I_2SD	PERGTBCH2I_1SD
PERGTBCH2I_2SD	RAT1_MEAN	RAT1N_MEAN	RAT2_MEAN
RAT2_MEDIAN	RAT2_SD	RAT2N_MEAN	RAT2N_MEDIAN	REGR
SUM_MEAN	SUM_MEDIAN	TOT_BPIX	TOT_SPIX	X_COORD	Y_COORD
TOP	BOT	LEFT	RIGHT	SECTOR	SECTORROW	SECTORCOL	SOURCE
PLATE	PROW	PCOL	FAILED	IS_VERIFIED	IS_CONTAMINATED
LUID
1	13762	IMAGE:753234	ZFX	**zinc finger protein,
X-linked	Hs.2074	AA406372						121	116		475	1092	732		
		389	360		330	672	1002			.85		0	.5			1.499	88		80	
.649	.707	1.541			1.415		1.515			511	120			67	79	35	47
1	1	1	GF200:96(1A1):384(1A1)	3	A	1	0	Y	U	500001
2	13766	IMAGE:50794	ZNF133	zinc finger protein 133
(clone pHZ-13)	Hs.78434	H17047						123	118		620	771
390					404	381		350	358	708			.78		0	-.792			.714	77	
64		1.59	1.732	.629			.577		.579			346	120			66	78	51
63	1	1	2	GF200:96(1A3):384(1A5)	3	A	5	0	Y	U	500003
3	13770	IMAGE:302190	MLLT2	**myeloid/lymphoid or
mixed-lineage leukemia (trithorax (Drosophila)
homolog); translocated to, 2	Hs.114765	N77807						131
122		440	563	194					390	369		339	178	517			.49		0
-1.305			.535	79		43		2.268	2.471	.441			.405		.406		
333	120			66	78	65	77	1	1	3	GF200:96(1A5):384(1A9)	3	A
9	0	Y	U	500005


--- "michael watson (IAH-C)"
<michael.watson at bbsrc.ac.uk> wrote:

> Can you tell me if these are real Excel files or
> just text files with a
> .xls extension? 
> 
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On
> Behalf Of Srinivas
> Iyyer
> Sent: 29 September 2005 00:00
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] problem reading GenePix files with
> .XLS extension
> 
> Hello:
> 
> 
> I am a fist time trying to analyze cdna data and
> right at the first step
> i was bombed.  can any one please help me:
> 
> 
> >library(Biobase)
> >library(marray)
> >samples =
> read.phenoData("phenodata.txt",header=TRUE,
> as.is = TRUE)
> > files = samples$fileName
> 
> spree of errors starts here:
> 
> ## the .XLS files are downloaded from Garber_lung
> data. 
> ## software used in GenePix
> ## path : I am using windows based R so changed the
> ## directory to
> where all my .XLS files area locatd
> 
> > mdata = read.GenePix(files, path=".")
> Error in if (skip > 0) readLines(file, skip) : 
>         missing value where TRUE/FALSE needed
> 
> 
> >mdata = read.GenePix(files, ext = 'xls')
> Error in if (skip > 0) readLines(file, skip) : 
>         missing value where TRUE/FALSE needed
> 
> 
> > mdata = read.marrayRaw(files,ext = "xls")
> Error in if (is.na(pattern)) { : argument is of
> length zero
> 
> > nmdata = read.marrayRaw(nfs, ext="xls")
> Error in if (is.na(pattern)) { : argument is of
> length zero
> > nmdata = read.marrayRaw(nfs, ext="xls", skip = 22)
> Reading ...  ./shu058.248-97_LCLC.xls
> Error in read.table(f, skip = skip2, header = TRUE,
> sep = sep, quote =
> quote,  : 
>         unused argument(s) (ext ...)
> 
> 
> How do I read these XLS files and retain all the
> inforamtion. 
> 
> can any one please give R commands till I get to
> normalization procedure. 
> 
> Thank you
> 
> srini
> 
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